From chemistry-request@ccl.net Fri Feb  4 08:56:27 2005
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From: "Gabor I. Csonka" <csonka <> web.inc.bme.hu>
To: <chemistry <> ccl.net>
Subject: CCL: dft question on sugar
Date: Fri, 4 Feb 2005 14:56:27 +0100
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Probably you can build on my earlier work too.
In general I can say that we should distinguish between short-range part of
the van der Waals (vdW) interaction and the long range part. The short range
part can be well described with non empirical functionals as PBE or TPSS.
The long range part not, it requires correction.

In general, the strong (and short) H-bonds can be reasonably described with
DFT functionals as B3PW91 or B3LYP provided that a reasonable basis set is
used I suggest 6-31+G(d,p) or 6-311+G(d,p). Reference:
Csonka, G. I. Proper basis set for quantum mechanical studies of potential
energy surfaces of carbohydrates 
J. Mol. Struct. (THEOCHEM),  2002, 584, 1-4.

Lot of other references are summarized in (some of them are preprint):
http://web.inc.bme.hu/~csonka/p96.html

Best regards, Gabor I. Csonka

> -----Original Message-----
> Hi I want to know if there are someone expert in DFT calculation methods
> on
> carbohydrates?
> 
> My question is: which  is or which are the best functionals for dft that
> describe correctly hydrogen bond and weak interaction like van der walls
> etc
> in sugar moieties?
> 
> Now I9m using b3lyp but it under estimate that kind of forces in my
> experiments...while hf overestimate these effects.
> 
> 




From chemistry-request@ccl.net Thu Feb  3 18:29:10 2005
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Subject: about MM+ ff in Hyperchem
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Dear all,

I have a question about the MM+ force field in Hyperchem. Is there any
difference between MM+ and Alliger's MM2 force field? E.g., if I have some
parameters developed for MM+ in Hyperchem, can I directly use them in MM2
ff (eg in TINKER)?

Thanks a lot!

Jeny




From chemistry-request@ccl.net Fri Feb  4 02:02:49 2005
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Date: Fri, 04 Feb 2005 08:59:22 +0200
From: Ulrike Salzner <salzner_at_fen.bilkent.edu.tr>
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Hello,
thanks to all the people who responded. The answers are very helpful to 
me. I also got inquiries to post a summary. It is found below.

Here my thoughts.
1) Does your software support dual processing.  This used to be called
vector processing.
2) If funds are short, put your money into as much memory as possible.
Ab initio programs are memory hogs.  A single very fast processor and
lots of RAM is probably better than two processors with minimal RAM.

Wayne E. Steinmetz



Hello,

we recently built a 12 processor cluster mainly running jaguar (due to its speed), but also gaussian, and had to decide between similar alternatives (we are now running dual athlon cpu's). In fact (regardingless on what x86 processors we are looking), it seems to be a decision on the question, if you want to run dual cpu nodes or a single cpu nodes and not if a xeon has much more power than a p4 cpu. (we had a dual xeon cluster, single p4, quad alpha (Tru64) and so on for some small benchmark tests). I think, after a look at the benchmars results, that at the end you will find gaussian running fine on xeons aswell as on p4, there will be small differences due to cache size, core-speed and so on but this isn't that remarkable point. But, what really counts is the parallelization efficiency between shared memory architecture (SMP, i.e. dual cpu) and parallelization using any sort of network interface. SMP is remarkably faster, giving you more performance even running two slower cpu's on one board in compasision to two faster single cpus on two single boards (and a xeon will anyway be faster than a p4 at the same speed). So if you plan to run jobs which can be parallelized (and this normally is the reason of such a cluster) I would always prefer using as less nodes as possible and as much cpu's as possible in one node. Normal geometry optimizations are parallelized nicely, so SMP is worth its money. I'm not sure about all features of gaussian 03, but commonly 2nd derivatives are harder to parallelize, so if you focus in your work on a lot of 2nd derivatives, i.e IR frequencies etc., you will be probably be more happy with a lot of machines each computing just one job (in case you do this on dual-cpu machines (2 jobs on each machine) you will get less performance because of memory-throughput, disk-acess and other bottle necks). But you should also take into account, that usually not all computations are parallelized through network-interface, due to large communication data. So there probably will be several things that can only be parralelized on an SMP system.

In short: If you do a lot of standard calculations (geometry optimizations, which of course often is the time-comsuming part even if you're interested in any details later on), you're happy with dual-cpu nodes. If you mainly have any special interest take a look at the handbook in how far this feature can be parallelized at all (if not, you'll be glader with single cpu machines) or only with SMP architecture (giving you the maximum of 2 cpu's anyway).

Regards

Eike Huebner

If infrastructure (cooling, electricity, maintenance) isn't an issue and you have Linda for parallel calculations, then I would
suggest the single processor P IV's.  With a single CPU configuration, you'll get more bandwidth to memory and disk for each
calculation.  

Also, you can get some significant speedup's by compiling Gaussian using the Intel compiler and math libraries which I believe are
free for educational institutions.

I would only choose the Xeon's if you have limited electrical amps.  Also, you'll have half as many machines to administrate and/or
fix.

Are you sure that the prices that you quoted have the same RAM per processor?

Joseph


I would suggest that the only way to know would be to test several
systems.  The problem here is to avoid comparing apples with oranges.
So perhaps you have a "typical job".  Why not ask people in the CCL to
run the job and then compare the run times.
  I like the dual Xeon.  Once Gaussian is compiled and running, it is
trivial to make the workstation understand NPROCS=2.  So now I have
about 1.8 times the speed of a single processor.  The next trick is to
load up the machine with memory.  This saves all the calls to temp
storage on the harddrive.
  Another thing to consider is that 64 bit processors are available.
This should be a big help in solving the 16 gB storage problem of a 32
bit processor.  Unfortunately there hasn't been much discussion here
about these new machine running Gaussian.

Hallo,

bei diesem Gleichstand wuerde ich das Dualgeraet vorziehen, denn dann kann
man auch Paralleljobs auf zwei Prozessoren (Gaussian, Amber etc) ohne
aufwendige Netzinfrastruktur rechnen, was sich bei groesseren Rechnungen
wirklich bezahlt macht.

Schoene Gruesse,

Anselm Horn


Hallo Ulrike,

Bei der Preislage wuerde ich die Einzelprozessormaschinen bevorzugen.
Hier eine Liste von Argumenten fuer und gegen beide Loesungen:

Vorteile der Dual-Prozessor-Loesung:
- Gaussian kann parallel laufen (ohne Linda), ein einzelner Job ist also
frueher fertig.
- Falls die sonstigen Resourcen (Speicher, Disk) pro Prozessor gleich
sind, kann ein Prozessor manchmal mehr als die Haelfte nutzen, was die
maximale Groesse einer Rechnung erhoeht.

Nachteil:
- Rechnungen mit G03 und aehnlichen Programmen sind sehr
speicherintensiv, und der Datendurchsatz zum Speicher ist oft der
limitierende Faktor. Eine Rechnung laeuft bis zu 30% langsamer, wenn auf
dem zweiten Prozessor etwas aehnliches laeuft. Dies ist noch schlimmer
fuer Festplattenzugriff. Wenn zwei I/O-intensive Prozesse gleichzeitig
laufen, sollten zwei Festplatten vorhanden sein (falls IDE, nicht am
selben Kabel).

Nachdem Deine PIVs ohnehin schon schneller sind als die Xeons, ist der
Unterschied in Performance wahrscheinlich das ausschlaggebende Argument.

Viele Gruesse,

  Herbert Fruechtl


In tests I ran this summer on G03 using 3.0 GHz Xeons/PIV's, I typically 
got a speedup of about ~1.7 when going from 1 to 2 processors on the same 
board, versus a speedup of ~1.95 on going from 1 to 2 processors when the 
2 processors were on different machines.  Other quantum codes using other 
parallel paradigms showed different numerical speedups, but the 
qualitative results were the same.

So in your case, the GHz/$ numbers are:
Two Xeons: 2 processors*2.8GHz*1.7speedup/$1960=.0047
Two PIV's: 2processors*3.2GHz*1.95speedup/($875*2)=.0071 <==Much better 
deal

Notes:
1) The tests were done with at least a 100Mb/s ethernet connection
2) The tests are not reflective of results for Opteron machines, where the 
speedup is basically 2.0 with both processors on a single board due to the 
better memory bus architecture (my own unprofessional opinion as to "why", 
but I think it is correct).
3) Test results seemed to hold qualitatively for 4 processor jobs, but I 
didn't test for any higher number of processors.
4) Buying more machines means more power, more space, more heat, more 
hardware failures, etc. that isn't factored into my simple cost/GHz number 
above.
5) Make sure you turn hyperthreading off.

Dave

Hi Ulrike,

Have you looked at spending money on faster BLAS and LAPACK code to go
with your G03 installation?  Faster numerical libraries can increase
CPU utilization, resulting in faster computation and quicker
turn-around for your compute jobs.  

If you are interested in trying OptimaNumerics Libraries which
incorporates a fast implementation of LAPACK, please do let me know.
I am attaching to this e-mail a copy of the slides with more details
on OptimaNumerics Libraries, the levels of performanc that we have
delivered and the values that we have delivered.  

Please do not hesitate to let me know if you have any questions.  I
can also be reached on the telephone at +44 798 941 7838.  

I look forward to hearing from you soon.

Thank you. 


Best wishes,
Kenneth Tan







From chemistry-request@ccl.net Fri Feb  4 05:08:27 2005
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Dear Colleagues,

A reminder of the upcoming two-day conference organized on behalf of the
Molecular Graphics and Modelling Society:-

Membranes and Membrane Proteins
April 4-6th 2005
St Catz College, Oxford
http://indigo1.biop.ox.ac.uk/mgms2005/

Early Abstract Deadline:  1st March 2005

Confirmed Speakers:-

Stephen White (UC Irvine)
Tony Watts (Oxford)
Klaus Schulten (UIUC)
Johan Eqvist (Uppsala)
Tjerk Straatsma (Pacific Northwest National Laboratory)
Paolo Carloni (SISSA, Trieste)
Didier Rognan (CNRS UMR, Strasbourg)
Bert de Groot (Max Planck Institute, Gvttingen)
Tommy Liljefors (Danish University of Pharmaceutical Sciences)
Velin Spassov (Accelrys)
Frank Blaney (GSK)
Frances Ashcroft (Oxford)


Many thanks,

Phil Biggin



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From: sa.cosco :: virgilio.it
Subject: protein-protein docking program
To: chemistry :: ccl.net
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Dear CCL'lers, 
I?m looking for a reliable (free) Protein-Protein docking program. I need
to dock two protein structures built by means of homology building, so it
becomes really tough to predict the binding orientation due to the uncertainty
connected with the accuracy of starting structures.
Any suggestion will be appreciated and, also, I would be really interested
in recent references to this field.
Best regards
Sandro






From chemistry-request@ccl.net Fri Feb  4 06:43:51 2005
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From: Ian Hovell <HOVELL{at}cetem.gov.br>
To: "'chemistry'" <chemistry{at}ccl.net>
Subject: CCL:Summary Maxdisk problem
Date: Fri, 4 Feb 2005 09:42:25 -0300 
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Dear CCLers,
I sent the following question:
=20
On running a MP2 opt+ freq job, part of which I have included below, I =
have
encountered a problem that is initially baffling to me. I am using =
G03W.
The job optimizes the molecule and passes on to the second internal
frequency job and fails claiming that the Maxdisk is not enough. I have
limited maxdisk in the default route file to 40000 MB, the disk size is =
73
GB, so I could increase the default value.
In the final table where the error is described it says that the
transformation will not fit into the maxdisk space. The table I assume =
is
using Words so it is calculating that the maxdisk being used is
947912704*8.3 GB (7.8Gb)=20
=20
Am I reading this table correctly and if so does anybody have any ideas =
of
what is going wrong.
=20
Thanks in advance
=20
The replies:
Dr. Hovell,
=20
   G03W is still a 32 bit Fortran application.  This limits the disk
for any one job to 16GB (2GW).  With Rev, C you can get this all in one
file.  With Rev. B you need to break it into 8 files as you have below.
There is some overhead for file system usage so I recommend 245MW =
rather
than 2GB.  Then MaxDisk is the sum of the 8 files, i.e. =
MaxDisk=3D1960MW
=20
   There is no way a single G03W job can effectively use all of the =
73GB
of disk you have.  If the above is not sufficient then you will need to
either 1) find a different machine with 64 bit addressing (not Windows)
or 2) use FREQ=3DNUMER which will take more CPU time but no more disk =
or
memory.
=20
   The value for MaxDisk is non-sense because it is rolling over the
sign and coming up on the other side.
Douglas J. Fox
Technical Support
Gaussian, Inc.
=20
fox{at}gaussian.com
It is true that the Maxdisk fails: you have only specified 16 GB in 8 x =

2gb segments, so you are hitting the limit there. A maximum useful=20
MaxDisk setting is thus 16GB - and this is an internal limit within G03 =

to the best of my knowledge.
Freq jobs with MP2 can be quite demanding...
Dr. Patrik Johansson
Condensed Matter Physics Group
Chalmers University of Technology
Sweden
2 things.  First there is a very good description of the MaxDisk =
keyword on
the Gaussian homepage.  Also, I've seen warnings on these pages about =
using
the rwf file storage right up to the max (i.e. in 2 gB chunks).  I have =
seen
suggestions here of using something more like 1800mb, or 1900mb.  I =
have no
idea why.
David M. Close
=20
Thanks Again
=20
Ian Hovell - Ph.D.=20
NUCLEO DE MODELAGEM MOLECULAR-NMM=20
Centro de Tecnologia Mineral - CETEM=20
Ministerio da Ci=EAncia e da Tecnologia- MCT=20
Avenida Ip=EA, No 900 - Cidade Universitaria=20
Ilha do Fund=E3o Rio de Janeiro RJ Brasil=20
CEP 21941-590=20
tel 00 55 (xx) 3865 7344 ou 3865 - 7216=20
Fax 00 55 (xx) 22602837 ou 2290-4286=20
e-mail hovell{at}cetem.gov.br
=20

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<body lang=3DPT-BR style=3D'tab-interval:35.4pt'>

<div class=3DSection1>

<p class=3DMsoNormal style=3D'mso-layout-grid-align:none'><font =
size=3D2 color=3Dblack
face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:"Courier New";
color:black;mso-ansi-language:EN-US'>Dear =
CCLers,<o:p></o:p></span></font></p>

<p class=3DMsoNormal style=3D'mso-layout-grid-align:none'><font =
size=3D2 color=3Dblack
face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:"Courier New";
color:black;mso-ansi-language:EN-US'>I sent the following =
question:<o:p></o:p></span></font></p>

<p class=3DMsoNormal style=3D'mso-layout-grid-align:none'><font =
size=3D2 color=3Dblack
face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:"Courier New";
color:black;mso-ansi-language:EN-US'><![if =
!supportEmptyParas]>&nbsp;<![endif]></span></font><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<p class=3DMsoNormal style=3D'mso-layout-grid-align:none'><font =
size=3D2 color=3Dblack
face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:"Courier New";
color:black;mso-ansi-language:EN-US'>On running a MP2 opt+ freq job, =
part of
which I have included below, I have encountered a problem that is =
initially
baffling to me. I am using G03W.</span></font><font size=3D2 =
color=3Dblack
face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:"Courier New";
color:black;mso-color-alt:windowtext;mso-ansi-language:EN-US'><o:p></o:p=
></span></font></p>

<p class=3DMsoNormal style=3D'mso-layout-grid-align:none'><font =
size=3D2 color=3Dblack
face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:"Courier New";
color:black;mso-ansi-language:EN-US'>The job optimizes the molecule and =
passes
on to the second internal frequency job and fails claiming that the =
Maxdisk is
not enough. I have limited maxdisk in the default route file to 40000 =
MB, the
disk size is 73 GB, so I could increase the default =
value.</span></font><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<p class=3DMsoNormal style=3D'mso-layout-grid-align:none'><font =
size=3D2 color=3Dblack
face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:"Courier New";
color:black;mso-ansi-language:EN-US'>In the final table where the error =
is
described it says that the transformation will not fit into the maxdisk =
space.
The table I assume is using Words so it is calculating that the maxdisk =
being
used is 947912704*8.3 GB (7.8Gb) </span></font><font size=3D2 =
color=3Dblack
face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:"Courier New";
color:black;mso-color-alt:windowtext;mso-ansi-language:EN-US'><o:p></o:p=
></span></font></p>

<p class=3DMsoNormal style=3D'mso-layout-grid-align:none'><font =
size=3D2 color=3Dblack
face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:"Courier New";
color:black;mso-ansi-language:EN-US'>&nbsp;</span></font><font size=3D2
color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<p class=3DMsoNormal style=3D'mso-layout-grid-align:none'><font =
size=3D2 color=3Dblack
face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:"Courier New";
color:black;mso-ansi-language:EN-US'>Am I reading this table correctly =
and if
so does anybody have any ideas of what is going =
wrong.</span></font><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<p class=3DMsoNormal style=3D'mso-layout-grid-align:none'><font =
size=3D2 color=3Dblack
face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:"Courier New";
color:black;mso-ansi-language:EN-US'>&nbsp;</span></font><font size=3D2
color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<div style=3D'border:none;border-bottom:solid windowtext =
.75pt;padding:0cm 0cm 1.0pt 0cm'>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;border:none;mso-border-bottom-alt:
solid windowtext .75pt;padding:0cm;mso-padding-alt:0cm 0cm 1.0pt =
0cm'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'>Thanks =
in
advance</span></font><font size=3D2 color=3Dblack face=3D"Courier =
New"><span
lang=3DEN-US style=3D'font-size:10.0pt;font-family:"Courier =
New";color:black;
mso-color-alt:windowtext;mso-ansi-language:EN-US'><o:p></o:p></span></fo=
nt></p>

</div>

<p class=3DMsoNormal><span class=3DEstiloDeCorreioEletrnico15><font =
size=3D2
color=3Dblack face=3DArial><span lang=3DEN-US =
style=3D'font-size:10.0pt;mso-bidi-font-size:
12.0pt;font-family:Arial;mso-ansi-language:EN-US'><![if =
!supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></font></span></p>=


<div style=3D'border:none;border-bottom:solid windowtext =
.75pt;padding:0cm 0cm 1.0pt 0cm'>

<p class=3DMsoNormal style=3D'border:none;mso-border-bottom-alt:solid =
windowtext .75pt;
padding:0cm;mso-padding-alt:0cm 0cm 1.0pt 0cm'><span
class=3DEstiloDeCorreioEletrnico15><font size=3D2 color=3Dblack =
face=3DArial><span
lang=3DEN-US =
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial;
mso-ansi-language:EN-US'>The =
replies:<o:p></o:p></span></font></span></p>

</div>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'>Dr. =
Hovell,</span></font><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'><![if =
!supportEmptyParas]>&nbsp;<![endif]></span></font><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'><span
style=3D"mso-spacerun: yes">&nbsp;&nbsp; </span>G03W is still a 32 bit =
Fortran
application.<span style=3D"mso-spacerun: yes">&nbsp; </span>This limits =
the disk</span></font><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'>for any =
one job
to 16GB (2GW).<span style=3D"mso-spacerun: yes">&nbsp; </span>With Rev, =
C you can
get this all in one</span></font><font size=3D2 color=3Dblack =
face=3D"Courier New"><span
lang=3DEN-US style=3D'font-size:10.0pt;font-family:"Courier =
New";color:black;
mso-color-alt:windowtext;mso-ansi-language:EN-US'><o:p></o:p></span></fo=
nt></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-ansi-language:EN-US'>file.<span
style=3D"mso-spacerun: yes">&nbsp; </span>With Rev. B you need to break =
it into 8
files as you have below.</span></font><font size=3D2 color=3Dblack
face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:"Courier New";
color:black;mso-color-alt:windowtext;mso-ansi-language:EN-US'><o:p></o:p=
></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'>There is =
some
overhead for file system usage so I recommend 245MW =
rather</span></font><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'>than =
2GB.<span
style=3D"mso-spacerun: yes">&nbsp; </span>Then MaxDisk is the sum of =
the 8 files,
i.e. MaxDisk=3D1960MW</span></font><font size=3D2 color=3Dblack =
face=3D"Courier New"><span
lang=3DEN-US style=3D'font-size:10.0pt;font-family:"Courier =
New";color:black;
mso-color-alt:windowtext;mso-ansi-language:EN-US'><o:p></o:p></span></fo=
nt></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'><![if =
!supportEmptyParas]>&nbsp;<![endif]></span></font><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'><span
style=3D"mso-spacerun: yes">&nbsp;&nbsp; </span>There is no way a =
single G03W job
can effectively use all of the 73GB</span></font><font size=3D2 =
color=3Dblack
face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:"Courier New";
color:black;mso-color-alt:windowtext;mso-ansi-language:EN-US'><o:p></o:p=
></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'>of disk =
you
have.<span style=3D"mso-spacerun: yes">&nbsp; </span>If the above is =
not
sufficient then you will need to</span></font><font size=3D2 =
color=3Dblack
face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:"Courier New";
color:black;mso-color-alt:windowtext;mso-ansi-language:EN-US'><o:p></o:p=
></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'>either =
1) find a
different machine with 64 bit addressing (not =
Windows)</span></font><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'>or 2) =
use
FREQ=3DNUMER which will take more CPU time but no more disk =
or</span></font><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-ansi-language:EN-US'>memory.</span></font><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'><![if =
!supportEmptyParas]>&nbsp;<![endif]></span></font><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'><span
style=3D"mso-spacerun: yes">&nbsp;&nbsp; </span>The value for MaxDisk =
is
non-sense because it is rolling over the</span></font><font size=3D2 =
color=3Dblack
face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:"Courier New";
color:black;mso-color-alt:windowtext;mso-ansi-language:EN-US'><o:p></o:p=
></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'>sign and =
coming
up on the other side.</span></font><font size=3D2 color=3Dblack =
face=3D"Courier New"><span
lang=3DEN-US style=3D'font-size:10.0pt;font-family:"Courier =
New";color:black;
mso-color-alt:windowtext;mso-ansi-language:EN-US'><o:p></o:p></span></fo=
nt></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'>Douglas =
J. Fox</span></font><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-ansi-language:EN-US'>Technical
Support</span></font><font size=3D2 color=3Dblack face=3D"Courier =
New"><span
lang=3DEN-US style=3D'font-size:10.0pt;font-family:"Courier =
New";color:black;
mso-color-alt:windowtext;mso-ansi-language:EN-US'><o:p></o:p></span></fo=
nt></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-ansi-language:EN-US'>Gaussian, =
Inc.</span></font><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'><![if =
!supportEmptyParas]>&nbsp;<![endif]></span></font><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<div style=3D'border:none;border-bottom:solid windowtext =
.75pt;padding:0cm 0cm 1.0pt 0cm'>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none;
border:none;mso-border-bottom-alt:solid windowtext .75pt;padding:0cm;
mso-padding-alt:0cm 0cm 1.0pt 0cm'><font size=3D2 color=3Dblack =
face=3D"Courier New"><span
lang=3DEN-US style=3D'font-size:10.0pt;font-family:"Courier =
New";color:black;
mso-ansi-language:EN-US'>fox{at}gaussian.com</span></font><font size=3D2
color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

</div>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'>It is =
true that
the Maxdisk fails: you have only specified 16 GB in 8 x =
</span></font><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'>2gb =
segments, so
you are hitting the limit there. A maximum useful </span></font><font =
size=3D2
color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'>MaxDisk =
setting
is thus 16GB - and this is an internal limit within G03 =
</span></font><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext;mso-ansi-language:
EN-US'><o:p></o:p></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'>to the =
best of
my knowledge.</span></font><font size=3D2 color=3Dblack face=3D"Courier =
New"><span
lang=3DEN-US style=3D'font-size:10.0pt;font-family:"Courier =
New";color:black;
mso-color-alt:windowtext;mso-ansi-language:EN-US'><o:p></o:p></span></fo=
nt></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'>Freq =
jobs with
MP2 can be quite demanding...</span></font><font size=3D2 color=3Dblack
face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:"Courier New";
color:black;mso-color-alt:windowtext;mso-ansi-language:EN-US'><o:p></o:p=
></span></font></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'>Dr. =
Patrik
Johansson</span></font><font size=3D2 color=3Dblack face=3D"Courier =
New"><span
lang=3DEN-US style=3D'font-size:10.0pt;font-family:"Courier =
New";color:black;
mso-color-alt:windowtext;mso-ansi-language:EN-US'><o:p></o:p></span></fo=
nt></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-ansi-language:EN-US'>Condensed Matter
Physics Group</span></font><font size=3D2 color=3Dblack face=3D"Courier =
New"><span
lang=3DEN-US style=3D'font-size:10.0pt;font-family:"Courier =
New";color:black;
mso-color-alt:windowtext;mso-ansi-language:EN-US'><o:p></o:p></span></fo=
nt></p>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none'><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;
font-family:"Courier New";color:black;mso-ansi-language:EN-US'>Chalmers
University of Technology</span></font><font size=3D2 color=3Dblack
face=3D"Courier New"><span lang=3DEN-US =
style=3D'font-size:10.0pt;font-family:"Courier New";
color:black;mso-color-alt:windowtext;mso-ansi-language:EN-US'><o:p></o:p=
></span></font></p>

<div style=3D'border:none;border-bottom:solid windowtext =
.75pt;padding:0cm 0cm 1.0pt 0cm'>

<p class=3DMsoNormal =
style=3D'mso-layout-grid-align:none;text-autospace:none;
border:none;mso-border-bottom-alt:solid windowtext .75pt;padding:0cm;
mso-padding-alt:0cm 0cm 1.0pt 0cm'><font size=3D2 color=3Dblack =
face=3D"Courier New"><span
lang=3DEN-GB style=3D'font-size:10.0pt;font-family:"Courier =
New";color:black'>Sweden</span></font><font
size=3D2 color=3Dblack face=3D"Courier New"><span lang=3DEN-GB =
style=3D'font-size:10.0pt;
font-family:"Courier =
New";color:black;mso-color-alt:windowtext'><o:p></o:p></span></font></p>=


</div>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
lang=3DEN-GB
style=3D'font-size:10.0pt;font-family:Arial;color:navy'>2 things.&nbsp; =
First
there is a very good description of the MaxDisk keyword on the Gaussian
homepage.&nbsp; Also, I&#8217;ve seen warnings on these pages about =
using the rwf
file storage right up to the max (i.e. in 2 gB chunks).&nbsp; I have =
seen
suggestions here of using something more like 1800mb, or 1900mb.&nbsp; =
I have
no idea why.</span></font><font size=3D2 color=3Dnavy =
face=3DArial><span lang=3DEN-GB
style=3D'font-size:10.0pt;font-family:Arial;mso-fareast-font-family:"Ari=
al Unicode MS";
color:navy'><o:p></o:p></span></font></p>

<div style=3D'border:none;border-bottom:solid windowtext =
.75pt;padding:0cm 0cm 1.0pt 0cm'>

<p class=3DMsoNormal style=3D'border:none;mso-border-bottom-alt:solid =
windowtext .75pt;
padding:0cm;mso-padding-alt:0cm 0cm 1.0pt 0cm'><span
class=3DEstiloDeCorreioEletrnico15><font size=3D2 color=3Dblack =
face=3DArial><span
lang=3DEN-GB =
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;font-family:Arial'>D=
avid
M. Close<o:p></o:p></span></font></span></p>

</div>

<p class=3DMsoNormal><span class=3DEstiloDeCorreioEletrnico15><font =
size=3D2
color=3Dblack face=3DArial><span lang=3DEN-GB =
style=3D'font-size:10.0pt;mso-bidi-font-size:
12.0pt;font-family:Arial'><![if =
!supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></font></span></p>=


<p class=3DMsoNormal><span class=3DEstiloDeCorreioEletrnico15><font =
size=3D2
color=3Dblack face=3DArial><span lang=3DEN-GB =
style=3D'font-size:10.0pt;mso-bidi-font-size:
12.0pt;font-family:Arial'>Thanks =
Again<o:p></o:p></span></font></span></p>

<p class=3DMsoNormal><span class=3DEstiloDeCorreioEletrnico15><font =
size=3D2
color=3Dblack face=3DArial><span lang=3DEN-GB =
style=3D'font-size:10.0pt;mso-bidi-font-size:
12.0pt;font-family:Arial'><![if =
!supportEmptyParas]>&nbsp;<![endif]><o:p></o:p></span></font></span></p>=


<p class=3DMsoNormal><!--[if supportFields]><font color=3Dblack><span =
lang=3DEN-GB=20
style=3D'color:black'><span =
style=3D'mso-element:field-begin'></span><span=20
style=3D"mso-spacerun: yes">&nbsp;</span>AUTOTEXTLIST \s =
&quot;Assinatura de=20
correio eletr=F4nico&quot; <span =
style=3D'mso-element:field-separator'></span></span></font><![endif]--><=
font
color=3Dblack><span lang=3DEN-GB style=3D'color:black'>Ian Hovell - =
Ph.D. </span></font><font
color=3Dblack><span lang=3DEN-GB =
style=3D'color:black;mso-color-alt:windowtext'><o:p></o:p></span></font>=
</p>

<p class=3DMsoNormal><font size=3D3 color=3Dblack face=3D"Times New =
Roman"><span
style=3D'font-size:12.0pt;color:black;mso-ansi-language:PT-BR'>NUCLEO =
DE
MODELAGEM MOLECULAR-NMM </span></font><font color=3Dblack><span =
style=3D'color:
black;mso-color-alt:windowtext;mso-ansi-language:PT-BR'><o:p></o:p></spa=
n></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3D"Times New =
Roman"><span
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;color:black;mso-ansi=
-language:
PT-BR'>Centro de Tecnologia Mineral - CETEM </span></font><font =
size=3D2
color=3Dblack><span =
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;color:black;
mso-color-alt:windowtext;mso-ansi-language:PT-BR'><o:p></o:p></span></fo=
nt></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3D"Times New =
Roman"><span
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;color:black;mso-ansi=
-language:
PT-BR'>Ministerio da Ci=EAncia e da Tecnologia- MCT </span></font><font =
size=3D2
color=3Dblack><span =
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;color:black;
mso-color-alt:windowtext;mso-ansi-language:PT-BR'><o:p></o:p></span></fo=
nt></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3D"Times New =
Roman"><span
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;color:black;mso-ansi=
-language:
PT-BR'>Avenida Ip=EA, No 900 - Cidade Universitaria </span></font><font =
size=3D2
color=3Dblack><span =
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;color:black;
mso-color-alt:windowtext;mso-ansi-language:PT-BR'><o:p></o:p></span></fo=
nt></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3D"Times New =
Roman"><span
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;color:black;mso-ansi=
-language:
PT-BR'>Ilha do Fund=E3o Rio de Janeiro RJ Brasil </span></font><font =
size=3D2
color=3Dblack><span =
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;color:black;
mso-color-alt:windowtext;mso-ansi-language:PT-BR'><o:p></o:p></span></fo=
nt></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3D"Times New =
Roman"><span
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;color:black;mso-ansi=
-language:
PT-BR'>CEP 21941-590 </span></font><font size=3D2 color=3Dblack><span
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;color:black;mso-colo=
r-alt:
windowtext;mso-ansi-language:PT-BR'><o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3D"Times New =
Roman"><span
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;color:black;mso-ansi=
-language:
PT-BR'>tel 00 55 (xx) 3865 7344 ou 3865 - 7216 </span></font><font =
size=3D2
color=3Dblack><span =
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;color:black;
mso-color-alt:windowtext;mso-ansi-language:PT-BR'><o:p></o:p></span></fo=
nt></p>

<p class=3DMsoNormal><font size=3D2 color=3Dblack face=3D"Times New =
Roman"><span
style=3D'font-size:10.0pt;mso-bidi-font-size:12.0pt;color:black;mso-ansi=
-language:
PT-BR'>Fax 00 55 (xx) 22602837 ou 2290-4286 </span></font><font =
color=3Dblack><span
style=3D'color:black;mso-color-alt:windowtext;mso-ansi-language:PT-BR'><=
o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D1 color=3Dblack face=3D"Times New =
Roman"><span
style=3D'font-size:9.0pt;mso-bidi-font-size:12.0pt;color:black;mso-ansi-=
language:
PT-BR'>e-mail hovell{at}cetem.gov.br</span></font><font size=3D1 =
color=3Dblack><span
style=3D'font-size:9.0pt;mso-bidi-font-size:12.0pt;color:black;mso-color=
-alt:
windowtext;mso-ansi-language:PT-BR'><o:p></o:p></span></font></p>

<p class=3DMsoNormal><!--[if supportFields]><font color=3Dblack><span =
lang=3DEN-GB=20
style=3D'color:black'><span =
style=3D'mso-element:field-end'></span></span></font><![endif]--><font
color=3Dblack><span lang=3DEN-GB style=3D'color:black'><![if =
!supportEmptyParas]>&nbsp;<![endif]></span></font><font
color=3Dblack><span lang=3DEN-GB =
style=3D'color:black;mso-color-alt:windowtext'><o:p></o:p></span></font>=
</p>

</div>

</body>

</html>

------_=_NextPart_001_01C50AB6.FAC0C470--


From chemistry-request@ccl.net Fri Feb  4 07:41:01 2005
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From: "Gabor I. Csonka" <csonka ## web.inc.bme.hu>
To: <chemistry ## ccl.net>
Cc: "'Nicola Catozzi'" <ctzncl ## unife.it>
Subject: RE: dft question on sugar
Date: Fri, 4 Feb 2005 11:37:32 +0100
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Probably you can build on my earlier work too.
In general I can say that we should distinguish between short-range part of
the van der Waals (vdW) interaction and the long range part. The short range
part can be well described with non empirical functionals as PBE or TPSS.
The long range part not, it requires correction.

In general, the strong (and short) H-bonds can be reasonably described with
DFT functionals as B3PW91 or B3LYP provided that a reasonable basis set is
used I suggest 6-31+G(d,p) or 6-311+G(d,p). Reference:
Csonka, G. I. Proper basis set for quantum mechanical studies of potential
energy surfaces of carbohydrates 
J. Mol. Struct. (THEOCHEM),  2002, 584, 1-4.

Lot of other references are summarized in (some of them are preprint):
http://web.inc.bme.hu/~csonka/p96.html

Best regards, Gabor I. Csonka

> -----Original Message-----
> Hi I want to know if there are someone expert in DFT calculation methods
> on
> carbohydrates?
> 
> My question is: which  is or which are the best functionals for dft that
> describe correctly hydrogen bond and weak interaction like van der walls
> etc
> in sugar moieties?
> 
> Now I9m using b3lyp but it under estimate that kind of forces in my
> experiments...while hf overestimate these effects.
> 
> 





From chemistry-request@ccl.net Fri Feb  4 08:30:27 2005
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Date: Fri,  4 Feb 2005 13:35:06 +0100
From: annek = = = chem.au.dk
To: chemistry = = = ccl.net
Subject: conformational search using MacroModel
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Is it possible to do a conformational search of a dihedral angle connecting two
non-bound molecules? We use the MacroModel program.

Mette & Anne



From chemistry-request@ccl.net Fri Feb  4 12:39:07 2005
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Date: Fri, 04 Feb 2005 17:24:55 +0100
From: "Dr. Bruno Catalanotti" <brucatal)at(unina.it>
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To: CHEMISTRY)at(ccl.net
Subject: CCL: deriving CFF91 partial charges
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dear CCLers,
I am trying to parametrize a protonated quinoline-based moiety with  the 
CFF91 Force Field (Insight2000.1 environment). CFF91 is not able to 
delocalize the additional charge on the aromatic ring, giving rise to 
the warning: "total formal charge does not equal total partial charge." 
In the case of CVFF Force Field, Accelrys suggests  to derive partial 
charges of protonated compounds  by comparing partial charges assigned 
by CVFF force field with those calculated by a MNDO semi-empirical 1 SCF 
calculations performed on the neutral and the ionized compounds.


Can anyone suggest me:
1 which semiempirical method is more suitable to derive CFF91 - 
compatible partial charges?
2 some references regarding methods to modify force field assigned 
partial charges?
3 any other alternative methods to calculate partial charges ?

Thank you in advance for help,
Best regards,
Bruno





From chemistry-request@ccl.net Fri Feb  4 13:25:57 2005
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Subject: Help interpreting G3B3 output in G03
From: Jim Pfaendtner <pfaendtner +*+ northwestern.edu>
To: chemistry +*+ ccl.net
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Hi all,

This is my output from a G3B3 calculation

 Temperature=    298.150000 Pressure=          1.000000
 E(ZPE)=           0.078779 E(Thermal)=        0.086957
 E(QCISD(T))=   -118.014612 E(Empiric)=       -0.064073
 DE(Plus)=        -0.009378 DE(2DF)=          -0.122879
 E(Delta-G3)=     -0.170882 E(G3-Empiric)=    -0.064073
 G3(0 K)=       -118.303045 G3 Energy=      -118.294867
 G3 Enthalpy=   -118.293923 G3 Free Energy= -118.338216


>From the Gaussian 03 manual and "Thermochemistry in Gaussian", I
understand E(Thermal) to be the "thermal correction to energy" or "Er +
Ev + Et + Ee".

I also understand that G3(0 K) + E(Thermal) = G3 Energy 
[(p97) of G03 manual]

In the above calculation, E(Thermal) = 0.087 au , but when you subtract
G3(0 K) from G3 Energy the result is = 0.0082 au - big difference.

I am pretty sure the mistake is on my part, but I need help seeing it.

Thanks







From chemistry-request@ccl.net Fri Feb  4 14:45:37 2005
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Subject: PROTEIN STRUCTURE & DRUG DISCOVERY WORKSHOP MARCH 17-18 2005 LA
 JOLLA CALIFORNIA 
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From chemistry-request@ccl.net Fri Feb  4 16:20:06 2005
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Hi all,

I have a related question.

I would like to be able to use HyperChem 5 to build molecules and then save 
them as *.mol files.  Then, I want to read them into Vega ZZ and run mopac 
on them.

My question is this.  Is there a format that I can save them as so the 
charges will be saved and be read into HyperChem?

Thanks in advance,
Richard





Richard L. Wood, Ph. D.
Computational Chemist
Hyrum, UT 84319

----- Original Message ----- 
From: <jz7[at]duke.edu>
To: <chemistry[at]ccl.net>
Sent: Thursday, February 03, 2005 12:36 PM
Subject: CCL:about MM+ ff in Hyperchem


> Dear all,
>
> I have a question about the MM+ force field in Hyperchem. Is there any
> difference between MM+ and Alliger's MM2 force field? E.g., if I have some
> parameters developed for MM+ in Hyperchem, can I directly use them in MM2
> ff (eg in TINKER)?
>
> Thanks a lot!
>
> Jeny
>
>
>
>
> -= This is automatically added to each message by the mailing script =-
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> 


From chemistry-request@ccl.net Fri Feb  4 17:50:59 2005
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Subject: Re: CCL:protein-protein docking program
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"Computational Chemistry List" <chemistry-request [] ccl.net> wrote on 
02/04/2005 01:13:22 AM:

> I?m looking for a reliable (free) Protein-Protein docking program. I 
need
> to dock two protein structures built by means of homology building, so 
it
> becomes really tough to predict the binding orientation due to the 
uncertainty
> connected with the accuracy of starting structures.
> Any suggestion will be appreciated and, also, I would be really 
interested
> in recent references to this field.

To see what is available, you may want to take a look at:

Janin J. 2005. Assessing predictions of protein-protein interaction: The 
CAPRI experiment. Prot Sci 14: 278

One of the programs mentioned is ZDOCK.  The web page for it is 
http://zlab.bu.edu/zdock/index.shtml.

Good luck,
Jeff

--
Jeffrey L. Nauss, Ph.D.
Lead Training Scientist
Accelrys
10188 Telesis Court, Suite 100
San Diego, CA 92121-4779

Phone: +1-858-799-5555
Fax: +1-858-799-5100
http://www.accelrys.com/training

--=_alternative 007540FD88256F9E_=
Content-Type: text/html; charset="US-ASCII"


<br><font size=2><tt>&quot;Computational Chemistry List&quot; &lt;chemistry-request [] ccl.net&gt;
wrote on 02/04/2005 01:13:22 AM:<br>
<br>
&gt; I?m looking for a reliable (free) Protein-Protein docking program.
I need<br>
&gt; to dock two protein structures built by means of homology building,
so it<br>
&gt; becomes really tough to predict the binding orientation due to the
uncertainty<br>
&gt; connected with the accuracy of starting structures.<br>
&gt; Any suggestion will be appreciated and, also, I would be really interested<br>
&gt; in recent references to this field.<br>
</tt></font>
<br><font size=2><tt>To see what is available, you may want to take a look
at:</tt></font>
<br>
<br><font size=3 face="Arial">Janin J. 2005. Assessing predictions of protein-protein
interaction: The CAPRI experiment. <i>Prot Sci</i> 14: 278</font>
<br>
<br><font size=2><tt>One of the programs mentioned is ZDOCK. &nbsp;The
web page for it is http://zlab.bu.edu/zdock/index.shtml.</tt></font>
<br>
<br><font size=2><tt>Good luck,</tt></font>
<br><font size=2><tt>Jeff</tt></font>
<br>
<br><font size=2 face="sans-serif">--<br>
Jeffrey L. Nauss, Ph.D.<br>
Lead Training Scientist<br>
Accelrys<br>
10188 Telesis Court, Suite 100<br>
San Diego, CA 92121-4779<br>
<br>
Phone: +1-858-799-5555<br>
Fax: +1-858-799-5100<br>
http://www.accelrys.com/training</font>
<br>
--=_alternative 007540FD88256F9E_=--


From chemistry-request@ccl.net Fri Feb  4 18:25:36 2005
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From: "Bienstock, Rachelle (NIH/NIEHS)" <biensto1 *o* niehs.nih.gov>
To: "'CHEMISTRY *o* ccl.net'" <CHEMISTRY *o* ccl.net>
Cc: "'sa.cosco *o* virgilio.it'" <sa.cosco *o* virgilio.it>
Subject: CCL: protein-protein docking program
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Hi Sandro:

Take a look at the CAPRI (Critical Assessment of Predicted
Interactions)webpage http://capri.ebi.ac.uk/
and the Proteins: Structure, Function and Genetics Issue Vol 52 No. 1
(2003).

These are the groups who have protein-protein docking programs available who
competed at CAPRI:

Abagyan Scripps Research Institute, La Jolla, CA 
Camacho Boston University, Boston,MA 
Eisenstein Weizmann Institute, Rehovot, Israel 
Fitzjohn-Bates Cancer Research UK, London,UK 
Gardiner Sheffield University,UK 
Gray-Baker University of Washington, Seattle,WA
Mustard University of Aberdeen,UK  
Norel Columbia University, New York,NY 
Olson Scripps Research Institute, La Jolla, CA 
Palma-Krippahl Universitade Nova, Lisboa, Portugal 
Ritchie University of Aberdeen,UK 
Shoichet Northwestern University, Chicago, 
Sternberg-Smith Imperial College, London,UK 
Ten Eyck UCSD, La Jolla, CA All 
Umemaya Kitasato University, Kitasato, Japan 
Vakser SUNY, Stony Brook,NY 
Valencia Universitad Autonoma, Madrid, Spain 
Wang Beijing Polytechnic University, Beijing, China 
Weng Boston University, Boston,MA 
Wolfson-Nussinov Tel Aviv University, Israel-NCI, Frederick,MD 

I'm sure some or all of them have websites where they may distribute their
software.
I don't know if Weng at Boston University distributes ZDOCK for free any
more as
it is now a product in the commercial Accelrys software suite.

Good luck, perhaps you can give some feedback on how the methods work....

Rachelle

Dr. Rachelle J. Bienstock
Molecular Modeling and Structural Biochemistry
National Institutes of Health (NIH)
National Institute of Environmental Health Sciences (NIEHS)
ITSS
P.O. Box 12233 MD F0-011
Research Triangle Park, NC 27709
Tel: (919) 541-3397


-----Original Message-----
From: sa.cosco *o* virgilio.it [mailto:sa.cosco *o* virgilio.it]
Sent: Friday, February 04, 2005 4:13 AM
To: chemistry *o* ccl.net
Subject: CCL:protein-protein docking program
Importance: High


Dear CCL'lers, 
I?m looking for a reliable (free) Protein-Protein docking program. I need
to dock two protein structures built by means of homology building, so it
becomes really tough to predict the binding orientation due to the
uncertainty
connected with the accuracy of starting structures.
Any suggestion will be appreciated and, also, I would be really interested
in recent references to this field.
Best regards
Sandro






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