sapna sarupria wrote:
Hello,
The simulation does not run even for one step and therefore, it is not
possible for me to check any of the components such as energy,
temperature etc. There is no error message except for "segmentation
fault". It does the same thing if I try to energy minimize the system
instead of running an MD simulation. The corresponding mdp file is
pasted below:
cpp = /lib/cpp
constraints = none
integrator = steep
nstcgsteep = 500
emtol = 500.0
emstep = 0.001
vdwtype = user
energygrps = POL
energygrp_table = POL POL
The commands I use are as follows:
grompp -f em.mdp -p 25mer_wca_vac.top -c 3.5ns.gro
mdrun -s topol.tpr -table table.xvg
Maybe you should make the table way longer. IIRC this is in vacuum with
no cutoffs. Then the interactions should still fall within the length of
the table.
Regards
Sapna
On Wed, Jul 16, 2008 at 10:08 AM, David van der Spoel
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote:
sapna sarupria wrote:
Hello,
Thanks David for your response. Actually I have used the same
tables for simulations of the polymer in water and have had no
problem with them. Those simulations run for 4 ns without a
problem. So the tables are correct and I am sure of that. I am
not using the CVS version and so I give the energy and second
derivative in the table. I have used user-defined tables in the
past and so the setup is correct in terms of changing the mdp
file and the top file. The problem seems to be more system
specific (meaning vacuum) than user error specific. Can you
suggest any other thing that may be the problem.
Have you checked energy components, temperature etc.?
Thanks a lot for your help.
Regards
Sapna
On Wed, Jul 16, 2008 at 9:23 AM, David van der Spoel
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> wrote:
sapna sarupria wrote:
---------- Forwarded message ----------
From: *sapna sarupria* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
<mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>>>
Date: Tue, Jul 15, 2008 at 9:16 AM
Subject: Using user-tables for simulations in vacuum
To: Discussion list for GROMACS users
<gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>> <mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>>>>
Hello users,
I am trying to do a simulation of a polymer chain (which is
simply a bead of unified methane molecules) in vacuum using
user-defined tables. The interactions are
Weeks-Chandler-Andersen instead of Lennard-Jones.
However, when
I run the simulations, mdrun gives me a segmentation
fault. When
I run simulations for the exact same configurations
without the
tables (and therefore using VdW) the simulations run fine. In
addition, the starting configurations were obtained after 3ns
simulations of the polymer in water.
So I was wondering if there is any issue with using
user-defined
tables with simulations in vacuum. If not do you have any
idea
what could be going wrong.
Some details of the mdp file:
1. pbc is turned off.
2. there is no pressure coupling.
3. center of mass removal is set to angular.
4. temperature is 298 K and berendsen thermostat is used.
5. energy groups and table are defined (correctly).
6. the cut-offs are set to 1.0nm (box size is larger than
4 nm).
7. no constraints are being used.
Most obvious error source is the table itself. Do you use the CVS
version? In that case you should provide energy and force,
otherwise
energy and second derivative. Distance units are in nm.
Compare to
existing tables in share/gromacs/top
Thank you
Regards
Sapna
-- Sapna Sarupria
Ph.D. Student - Chemical Engineering
Rensselaer Polytechnic Institute
Troy, New York 12180
U.S.A.
Ph#: (518)276-3031
Life isn't about finding yourself. Life is about creating
yourself.
George Bernard Shaw.
Dare to Dream
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--
Sapna Sarupria
Ph.D. Student - Chemical Engineering
Rensselaer Polytechnic Institute
Troy, New York 12180
U.S.A.
Ph#: (518)276-3031
Life isn't about finding yourself. Life is about creating yourself.
George Bernard Shaw.
Dare to Dream
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
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--
Sapna Sarupria
Ph.D. Student - Chemical Engineering
Rensselaer Polytechnic Institute
Troy, New York 12180
U.S.A.
Ph#: (518)276-3031
Life isn't about finding yourself. Life is about creating yourself.
George Bernard Shaw.
Dare to Dream
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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