From owner-chemistry@ccl.net Mon Sep  1 11:00:00 2008
From: "Kshatresh Dutta Dubey kshatresh%x%gmail.com" <owner-chemistry%%server.ccl.net>
To: CCL
Subject: CCL: problem in dynamics
Message-Id: <-37691-080901053447-9141-w0OTmlK8tzb5w6a91DEmag%%server.ccl.net>
X-Original-From: "Kshatresh Dutta Dubey" <kshatresh]|[gmail.com>
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Sent to CCL by: "Kshatresh Dutta Dubey" [kshatresh/./gmail.com]
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Dear all,

I am using Maestro, Impact to study molecular dynamics of a system..After
some steps it is giving error like " fail to update box size".  log file is
given below..


Total number of atoms = 12382
%IMPACT-I (runmd): Using the Verlet integrator
%IMPACT-I (runmd): Translational and rotational motions for the system are
removed
Step number: 0 Non-bonded count: 2198814
Temp E-tot E-kin E-pot ETCM ERCM Pressure Density
4.50345E+02 2.72356E+16 1.10456E+04 2.72356E+16 1.82883E+03 1.78142E+03
3.65649E+02 3.94448E-01
%IMPACT-I (runmd): Translational and rotational motions for the system are
removed; new initial conditions are:
Step number: 0 Non-bonded count: 2198814
4.50345E+02 2.72356E+16 1.10456E+04 2.72356E+16 1.82883E+03 1.78142E+03
3.65649E+02 3.94448E-01
nblistsetbox(): mmnblist is not initialized call nblistinit() first.
%IMPACT-E (die): At line 39
%IMPACT-E: xyzscale(): Unable to update box size!


kindelly help me to overcome this error..
Thanks in advance
with regards....

Kshatresh

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Dear all,<br><br>I am using Maestro, Impact to study molecular dynamics of a system..After some steps it is giving error like &quot; fail to update box size&quot;. &nbsp;log file is given below..<br> <br><br>Total number of atoms = 12382<br>
%IMPACT-I (runmd): Using the Verlet integrator<br>%IMPACT-I (runmd): Translational and rotational motions for the system are removed<br>Step number: 0 Non-bonded count: 2198814<br>Temp E-tot E-kin E-pot ETCM ERCM Pressure Density<br>
4.50345E+02 2.72356E+16 1.10456E+04 2.72356E+16 1.82883E+03 1.78142E+03 3.65649E+02 3.94448E-01<br>%IMPACT-I (runmd): Translational and rotational motions for the system are removed; new initial conditions are:<br>Step number: 0 Non-bonded count: 2198814<br>
4.50345E+02 2.72356E+16 1.10456E+04 2.72356E+16 1.82883E+03 1.78142E+03 3.65649E+02 3.94448E-01<br>nblistsetbox(): mmnblist is not initialized call nblistinit() first.<br>%IMPACT-E (die): At line 39<br>%IMPACT-E: xyzscale(): Unable to update box size!<br>
<br><br>kindelly help me to overcome this error..<br>Thanks in advance<br>with regards....<br><br>Kshatresh<br><br>

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From owner-chemistry@ccl.net Mon Sep  1 14:56:01 2008
From: "Pablo Englebienne pablo.englebienne*mcgill.ca" <owner-chemistry{=}server.ccl.net>
To: CCL
Subject: CCL: problem in dynamics
Message-Id: <-37692-080901144318-29160-K0H6fmH09svLzZmAjboa7w{=}server.ccl.net>
X-Original-From: Pablo Englebienne <pablo.englebienne]~[mcgill.ca>
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Date: Mon, 01 Sep 2008 14:42:22 -0400
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Sent to CCL by: Pablo Englebienne [pablo.englebienne_+_mcgill.ca]
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Hi Kshatresh,

I've never used Impact for MD, but I can tell that some values seem very 
high from the beginning:

Step number: 0 Non-bonded count: 2198814
Temp        E-tot       E-kin       E-pot       ETCM        ERCM        
Pressure    Density
4.50345E+02 2.72356E+16 1.10456E+04 2.72356E+16 1.82883E+03 1.78142E+03 
3.65649E+02 3.94448E-01
^^^^^^^^^^^ ^^^^^^^^^^^ ^^^^^^^^^^^ ^^^^^^^^^^^

In particular, the E-pot is abnormaly high. Check your initial system 
for any bad clashes, superpositions, etc. Also, are you trying to run 
your simulation at 450K? I'm not sure what your system is, but you 
should try to heat it up slowly at first. Although designed for Amber 
MD's, I found these tutorials very useful:

http://amber.scripps.edu/tutorials/

The first tutorial (TUTORIAL B1: Simulating a small fragment of DNA 
<http://amber.scripps.edu/tutorials/basic/tutorial1/index.htm>) deals 
with these issues.

Cheers!

-- 
Pablo Englebienne, PhD Student, Moitessier research group
Department of Chemistry, McGill University
801 Sherbrooke Street West
Otto Maass bldg, room 206
H3A 2K6 Montréal, Québec, Canada
Tel (514) 398-5501    Fax (514) 398-2382

"Progress is made by lazy men looking for easier ways to do things." - Robert A. Heinlein



Kshatresh Dutta Dubey kshatresh%x%gmail.com wrote:
> Dear all,
>
> I am using Maestro, Impact to study molecular dynamics of a 
> system..After some steps it is giving error like " fail to update box 
> size".  log file is given below..
>
>
> Total number of atoms = 12382
> %IMPACT-I (runmd): Using the Verlet integrator
> %IMPACT-I (runmd): Translational and rotational motions for the system 
> are removed
> Step number: 0 Non-bonded count: 2198814
> Temp E-tot E-kin E-pot ETCM ERCM Pressure Density
> 4.50345E+02 2.72356E+16 1.10456E+04 2.72356E+16 1.82883E+03 
> 1.78142E+03 3.65649E+02 3.94448E-01
> %IMPACT-I (runmd): Translational and rotational motions for the system 
> are removed; new initial conditions are:
> Step number: 0 Non-bonded count: 2198814
> 4.50345E+02 2.72356E+16 1.10456E+04 2.72356E+16 1.82883E+03 
> 1.78142E+03 3.65649E+02 3.94448E-01
> nblistsetbox(): mmnblist is not initialized call nblistinit() first.
> %IMPACT-E (die): At line 39
> %IMPACT-E: xyzscale(): Unable to update box size!
>
>
> kindelly help me to overcome this error..
> Thanks in advance
> with regards....
>
> Kshatresh
>

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Hi Kshatresh,<br>
<br>
I've never used Impact for MD, but I can tell that some values seem
very high from the beginning:<br>
<br>
<tt>Step number: 0 Non-bonded count: 2198814<br>
Temp &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; E-tot &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; E-kin &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; E-pot &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ETCM &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; ERCM &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Pressure&nbsp;&nbsp;&nbsp; Density<br>
4.50345E+02 2.72356E+16 1.10456E+04 2.72356E+16 1.82883E+03 1.78142E+03
3.65649E+02 3.94448E-01<br>
^^^^^^^^^^^ ^^^^^^^^^^^ ^^^^^^^^^^^ ^^^^^^^^^^^<br>
</tt><br>
In particular, the E-pot is abnormaly high. Check your initial system
for any bad clashes, superpositions, etc. Also, are you trying to run
your simulation at 450K? I'm not sure what your system is, but you
should try to heat it up slowly at first. Although designed for Amber
MD's, I found these tutorials very useful:<br>
<br>
<a class="moz-txt-link-freetext" href="http://amber.scripps.edu/tutorials/">http://amber.scripps.edu/tutorials/</a><br>
<br>
The first tutorial (<a
 href="http://amber.scripps.edu/tutorials/basic/tutorial1/index.htm">TUTORIAL
B1: Simulating a small fragment of DNA</a>) deals with these issues.<br>
<br>
Cheers!<br>
<pre class="moz-signature" cols="72">-- 
Pablo Englebienne, PhD Student, Moitessier research group
Department of Chemistry, McGill University
801 Sherbrooke Street West
Otto Maass bldg, room 206
H3A 2K6 Montr&eacute;al, Qu&eacute;bec, Canada
Tel (514) 398-5501    Fax (514) 398-2382

"Progress is made by lazy men looking for easier ways to do things." - Robert A. Heinlein
</pre>
<br>
<br>
Kshatresh Dutta Dubey kshatresh%x%gmail.com wrote:
<blockquote
 cite="mid:-id%234m4-37691-080901053447-9141-Wbn9gwMquYwgQLIB55vp%2FQ .. server.ccl.net"
 type="cite">Dear all,<br>
  <br>
I am using Maestro, Impact to study molecular dynamics of a
system..After some steps it is giving error like " fail to update box
size". &nbsp;log file is given below..<br>
  <br>
  <br>
Total number of atoms = 12382<br>
%IMPACT-I (runmd): Using the Verlet integrator<br>
%IMPACT-I (runmd): Translational and rotational motions for the system
are removed<br>
Step number: 0 Non-bonded count: 2198814<br>
Temp E-tot E-kin E-pot ETCM ERCM Pressure Density<br>
4.50345E+02 2.72356E+16 1.10456E+04 2.72356E+16 1.82883E+03 1.78142E+03
3.65649E+02 3.94448E-01<br>
%IMPACT-I (runmd): Translational and rotational motions for the system
are removed; new initial conditions are:<br>
Step number: 0 Non-bonded count: 2198814<br>
4.50345E+02 2.72356E+16 1.10456E+04 2.72356E+16 1.82883E+03 1.78142E+03
3.65649E+02 3.94448E-01<br>
nblistsetbox(): mmnblist is not initialized call nblistinit() first.<br>
%IMPACT-E (die): At line 39<br>
%IMPACT-E: xyzscale(): Unable to update box size!<br>
  <br>
  <br>
kindelly help me to overcome this error..<br>
Thanks in advance<br>
with regards....<br>
  <br>
Kshatresh<br>
  <br>
</blockquote>
</body>
</html>

--------------060009090609080305020706--


From owner-chemistry@ccl.net Mon Sep  1 18:45:01 2008
From: "Joaquin Barroso jbarrosof[*]comex.com.mx" <owner-chemistry.:.server.ccl.net>
To: CCL
Subject: CCL:G: G03: crystal polarizability and pbc
Message-Id: <-37693-080901153811-20586-VWKuqX6h0j14HwZeBT0pzw.:.server.ccl.net>
X-Original-From: "Joaquin  Barroso" <jbarrosof\a/comex.com.mx>
Date: Mon, 1 Sep 2008 15:38:07 -0400


Sent to CCL by: "Joaquin  Barroso" [jbarrosof!A!comex.com.mx]
Greetings everyone,

Is there a way to calculate the polarizability of a crystal using the PBC module in Gaussian03? Could you point me to a reasonable set of papers regarding this question? I've been having troubles trying to make one of these calculations to converge and i havent had the time to take a deeper look on how to propperly use the aforementioned module. 
Thanks to everyone for your kind help Best wishes,

Dr. Joaquin Barroso-Flores 
Centro de Investigacin en Polmeros, COMEX 
Marcos Achar Lobatn 2, Tepexpan, Mpo. de Acolman 
Mexico 
Tel Cel: 0445510072407 
Correos alternos: 
joaquin.barroso^a^gmail.com 
jbarroso^a^cip.org 
jbarrosof^a^comex.com.mx