From chemistry-request@ccl.net Mon Mar 21 06:29:35 2005
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Subject: CCL: references for AlQ3
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From: "Igor Avilov" <avilovi _()_ averell.umh.ac.be>
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Dear CCLers,

I'm sorry to post a technical question, but I will very much appreciate the references for the crystal structure and quantum-chemical calculations of tris(8-hydroxyquinolino) aluminum (AlQ3).

Best regards,
Igor Avilov.



From chemistry-request@ccl.net Mon Mar 21 02:41:18 2005
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Date: Mon, 21 Mar 2005 14:35:44 +0800
From: "Mingyue Zheng" <myzheng :: iris3.simm.ac.cn>
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Subject: open source for SASA calculations?
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Dear all,
	
I'm looking for code/program dealing with atomic solvent accessible surface area calculations (better in C++).
Glad to hear any information about that.
Thanks in advance! 



Best regards. 
  
************************************************
Mingyue Zheng,2005-03-21  
#555 Rd. Zuchongzhi, Zhangjiang Hi-Tech Park
Drug Discovery and Design Center
Shanghai Institute of Meteria Medica
Chinese Academy of Sciences
Shanghai 201203, China
Tel#:   +86-21-50806600-1201
E-mail: myzheng :: iris3.simm.ac.cn
************************************************



From chemistry-request@ccl.net Mon Mar 21 11:14:38 2005
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Subject: CCL: Re: open source for SASA calculations?
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> From owner-chemistry :: ccl.net Mon Mar 21 15:35:59 2005
Date: Mon, 21 Mar 2005 14:35:44 +0800
From: "Mingyue Zheng" <myzheng :: iris3.simm.ac.cn>
To: "chemistry :: ccl.net" <chemistry :: ccl.net>
Subject: CCL:open source for SASA calculations?

> I'm looking for code/program dealing with atomic solvent accessible surface area calculations (better in C++).
> Glad to hear any information about that.

Look to the ASV freeware (volumes and surfaces):
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html
(includes documentation and ref.)

Michel Petitjean                      Email: petitjean :: itodys.jussieu.fr
entropy :: mdpi.org                             ptitjean :: ccr.jussieu.fr
Editor-in-Chief of Entropy            http://www.mdpi.org/entropy
FIS2005 coordinator                   http://www.mdpi.org/fis2005
ITODYS (CNRS, UMR 7086)
1 rue Guy de la Brosse                Phone: +33 (0)1 44 27 48 57
75005 Paris, France.                  FAX  : +33 (0)1 44 27 68 14
http://petitjeanmichel.free.fr/itoweb.petitjean.html

From chemistry-request@ccl.net Mon Mar 21 11:13:26 2005
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Date: Mon, 21 Mar 2005 10:14:50 -0500
To: chemistry *o* ccl.net
Subject: CCL: Error in conformational analysis with MM3 in TINKER
From: "Reynier Suardiaz del Rio" <reynier *o* fq.uh.cu>
Organization: Universidad de la Habana
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  Dear CCL members

> I have used the MM3 force field included into TINKER package to perform  
> a MD of butane in a
> periodic solvent box of ethane.
> I generated this solvent box and included into it the butane molecule  
> with
> the program xyzedit included in the TINKER package. I runned the dynamic
> with the program dynamic of TINKER.
> The periodic solvent box of ethane is a cube of 200 angstroms of side  
> with
> 100 molecules
> The only keywords that I used are
> a-axis 250
> b-axis 250
> c-axis 250
> The dynamic were programed to run:
> 1e+11 Number of Dynamic Steps
> 1.0 femtosecond of Time Step Length
> 10000 picoseconds of Time between Dumps
> Isothermal-Isobaric (NPT) of Statistical Mechanical Ensembles
> 298 K of Temperature
> 1 atm of Preassure
> But the butane did not explore any other conformation than anti.
> I will be very grateful of receive some suggests of you to modify the
> conditions in order to improve the results.
> David Santos Carballal

-- 






              ______________________________

                 Reynier Suardiaz del RC-o
                 Dpto. de QuC-mica FC-sica
                 Facultad de QuC-mica
                 Universidad de la Habana
                 telf: (53-7) 878 0684
                 e-mail: reynier *o* fq.uh.cu
                 web: http://www.fq.uh.cu
              ______________________________


From chemistry-request@ccl.net Mon Mar 21 12:26:21 2005
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From: Ian Hovell <HOVELL :: cetem.gov.br>
To: "'chemistry'" <chemistry :: ccl.net>
Subject: CCL: Cpu time in Gaussian output
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Dear CCLers,
I was asked the other day about the meaning of the cpu time that Gaussian
reports at the end of a job. The value does not match with the actual time
of the calculation which can be worked out from the date stamps at the
beginning and end of the output file..
The explanation I gave was that it was the time taken for the calculation on
the cpu and the difference between that and the reported date stamps was the
time the computer was waiting to write to the hard disk, transfer data etc.
Would this be a reasonable explanation for the difference in values?
 
TIA
 
 
Ian Hovell - Ph.D. 
NUCLEO DE MODELAGEM MOLECULAR-NMM 
Centro de Tecnologia Mineral - CETEM 
Ministerio da Cincia e da Tecnologia- MCT 
Avenida Ip, No 900 - Cidade Universitaria 
Ilha do Fundo Rio de Janeiro RJ Brasil 
CEP 21941-590 
tel 00 55 (xx) 3865 7344 ou 3865 - 7216 
Fax 00 55 (xx) 22602837 ou 2290-4286 
e-mail hovell :: cetem.gov.br <mailto:hovell :: cetem.gov.br>  

 

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<META content="MSHTML 5.50.4937.800" name=GENERATOR></HEAD>
<BODY>
<DIV><FONT face=Arial size=2><SPAN class=058123115-21032005>Dear 
CCLers,</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=058123115-21032005>I was asked the 
other day about the meaning of the cpu time that Gaussian reports at the end of 
a job. The value does not match with the actual time of the calculation which 
can be worked out from the date stamps at the beginning and end of the output 
file..</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN class=058123115-21032005>The explanation I 
gave was that it was the time taken for the calculation on the cpu and the 
difference between that and the reported date stamps was the time the computer 
was waiting to write to the hard disk, transfer data etc. Would this be a 
reasonable explanation for the difference in values?</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN 
class=058123115-21032005></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=Arial size=2><SPAN 
class=058123115-21032005>TIA</SPAN></FONT></DIV>
<DIV><FONT face=Arial size=2><SPAN 
class=058123115-21032005></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=Arial size=2><SPAN 
class=058123115-21032005></SPAN></FONT>&nbsp;</DIV>
<DIV><FONT face=Arial size=2>Ian Hovell - Ph.D. <BR>NUCLEO DE MODELAGEM 
MOLECULAR-NMM <BR>Centro de Tecnologia Mineral - CETEM <BR>Ministerio da Cincia 
e da Tecnologia- MCT <BR>Avenida Ip, No 900 - Cidade Universitaria <BR>Ilha do 
Fundo Rio de Janeiro RJ Brasil <BR>CEP 21941-590 <BR>tel 00 55 (xx) 3865 7344 ou 
3865 - 7216 <BR>Fax 00 55 (xx) 22602837 ou 2290-4286 <BR>e-mail <A 
href="mailto:hovell :: cetem.gov.br">hovell :: cetem.gov.br</A> <BR></FONT></DIV>
<DIV>&nbsp;</DIV></BODY></HTML>

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From chemistry-request@ccl.net Mon Mar 21 14:08:00 2005
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From: "Andreas, , Heyden" <a.heyden !=! gmx.net>
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Subject: W:Activation barrier accuracy with B3LYP
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Hi,

I have heard that DFT in general underestimates activation barriers for chemical reactions. Does anyone know if this is also the case for hybrid functionals like B3LYP?
If anyone knows good references please let me know.

Regards,
Andreas


From chemistry-request@ccl.net Mon Mar 21 15:36:34 2005
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Date: Mon, 21 Mar 2005 11:36:29 -0800 (PST)
From: Joseph Han <jhh3851 !=! yahoo.com>
Reply-To: jhh3851 !=! yahoo.com
Subject: Re: CCL:Cpu time in Gaussian output
To: Ian Hovell <HOVELL !=! cetem.gov.br>, "'chemistry'" <chemistry !=! ccl.net>
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IO wait time is a valid explanation especially if there are large files that
are written and read such as during frequency or correlated wavefunction
techniques.

Another possibility is if you are running in parallel (SMP or Linda), depending
upon the particular operating system, the CPU time reported can be different. 
If might be the launching thread, one computation thread, or the total CPU
time. Also, if you are running in parallel, and one thread is delayed, then
there can be a difference in the total Wall time versus CPU time.

Joseph

--- Ian Hovell <HOVELL !=! cetem.gov.br> wrote:
> Dear CCLers,
> I was asked the other day about the meaning of the cpu time that Gaussian
> reports at the end of a job. The value does not match with the actual time
> of the calculation which can be worked out from the date stamps at the
> beginning and end of the output file..
> The explanation I gave was that it was the time taken for the calculation on
> the cpu and the difference between that and the reported date stamps was the
> time the computer was waiting to write to the hard disk, transfer data etc.
> Would this be a reasonable explanation for the difference in values?
>  
> TIA
>  
>  
> Ian Hovell - Ph.D. 
> NUCLEO DE MODELAGEM MOLECULAR-NMM 
> Centro de Tecnologia Mineral - CETEM 
> Ministerio da Cincia e da Tecnologia- MCT 
> Avenida Ip, No 900 - Cidade Universitaria 
> Ilha do Fundo Rio de Janeiro RJ Brasil 
> CEP 21941-590 
> tel 00 55 (xx) 3865 7344 ou 3865 - 7216 
> Fax 00 55 (xx) 22602837 ou 2290-4286 
> e-mail hovell !=! cetem.gov.br <mailto:hovell !=! cetem.gov.br>  
> 
>  
> 


From chemistry-request@ccl.net Mon Mar 21 13:17:46 2005
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Date: Mon, 21 Mar 2005 09:17:40 -0800 (PST)
From: Konstantin Kudin <konstantin_kudin = = = yahoo.com>
Subject: problems with the SCF convergence in Gaussian 03
To: chemistry = = = ccl.net
MIME-Version: 1.0
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 Hi all,

 This message is for those still suffering from the SCF convergence
problems in G03.

 The problems can happen when the system has lots of close in energy
electronic states.

 If the method is Hartree-Fock, or some hybrid functional (i.e.,
B3LYP), try the following options:

scf=(noincfock,conver=11,maxcyc=1025) iop(5/22=20)

 These options force the use of pure EDIIS which is more expensive but
has a better chance of converging to a low state. The cranked up
accuracy is needed to make the SCF run for a good number of cycles
which improves the chances to end up in a low state.

 With pure functionals (non-hybrid such as BLYP) one can end up with
fractional occupation numbers, so the skill required to converge
somewhere is higher (level shift is definitely needed). If there is
some interest in this, I can follow up with another message.

 Kostya


		
__________________________________ 
Do you Yahoo!? 
Yahoo! Mail - 250MB free storage. Do more. Manage less. 
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From chemistry-request@ccl.net Mon Mar 21 13:22:35 2005
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To: chemistry = = = ccl.net
Subject: Re: Getting hessian out of Gaussian jobs
References: <Pine.LNX.4.58.0503151853430.31133 = = = fili.ccmr.cornell.edu> <Pine.OSF.4.61.0503161417310.47940 = = = heavy.it.helsinki.fi>
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Tom Sundius wrote:

> The hessian stored in the checkpoint file. If you did not have the p 
> option on your
> route card ("#p...") you will not get the force constants listed (except 
> for
> the list in the archive part, which is obviously missing from your output).
> Unfortunately the NewZMat utility does not seem to have an option to output
> the force constants in the check point file, so I guess that you will have
> to run a simple freq calculation with freq=readfc and geom=check 
> guess=check, but it should be rather fast.
> 

You can use the formchk utility to format the checkpoint file, so you 
can read the hessian matrix stored inside. Take care, all units are 
atomic units, and being a symmetric matrix only one half is printed.

Regards,
Michele Lunelli




From chemistry-request@ccl.net Mon Mar 21 14:13:01 2005
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Date: Mon, 21 Mar 2005 10:12:55 -0800
From: Eric Hu <eric.y.hu !=! gmail.com>
Reply-To: Eric Hu <eric.y.hu !=! gmail.com>
To: chemistry !=! ccl.net
Subject: substrate exit from protein in Amber 8.0 TI vdw simulation
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Hi, I am trying to perturb a molecule to nothing in a protein binding
pocket. By looking at the pdb files at the end of each lambda run, the
molecule has migrated out of the protein when clambda is equal to
0.43738 or bigger. One explanation would be that the small molecule
with shrinking vdw radii do not have favorable interactions with
protein any more comparing to water molecules and expelled therefore.
Therefore I wonder if a weak restraint is needed in order to evaluate
the dV/dL ~ L integral. Thanks.

I suspect that this is true for all vdw perturbation calculations.

Eric

&cntrl
  ntr=0,
  nstlim =20000, nscm=2000, ntave=5000,
  ntx=1, irest=0, ntb=1, ntpr=100, tempi=300.0, ig=974651,
  ntp=0, taup=1.0,
  dt=0.001, nrespa=1,
  ntt=1, temp0 = 300., tautp=2.0,
  ntc=2, ntf=2, tol=0.000001,
  ntwr = 100, ntwx=100,
  icfe=1, klambda=6, clambda=0.99078,
 cut=9.0,
/