Re: [gmx-users] Using user-tables for simulations in vacuum

2008-07-18 Thread David van der Spoel 

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] > 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] 
>> wrote:

   sapna sarupria wrote:



   -- Forwarded message --
   From: *sapna sarupria* <[EMAIL PROTECTED]

   >
   

   >

Re: [gmx-users] Using user-tables for simulations in vacuum

2008-07-16 Thread sapna sarupria 
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

Regards
Sapna


On Wed, Jul 16, 2008 at 10:08 AM, David van der Spoel <[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] > wrote:
>>
>>sapna sarupria wrote:
>>
>>
>>
>>-- Forwarded message --
>>From: *sapna sarupria* <[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 > >>>
>>
>>
>>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
>>
>>
>>
>>  
>>
>>___
>>gmx-users mailing listgmx-users@gromacs.org
>>
>>http://www.gromacs.org/mailman/listinfo/gmx-users
>>Please search the archive at http://www.gromacs.org/search
>>before posting!
>>Please don't post (un)subscribe requests to the list. Use the
>>www interface or send it to [EMAIL PROTECTED]
>>.
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>>
>>
>>--David van der Spoel, Ph.D., Professor of Biology
>>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala
>> University.
>>Bo

Re: [gmx-users] Using user-tables for simulations in vacuum

2008-07-16 Thread David van der Spoel 

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] > wrote:


sapna sarupria wrote:



-- Forwarded message --
From: *sapna sarupria* <[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 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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Please search the archive at http://www.gromacs.org/search
before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php



-- 
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

___
gmx-users mailing listgmx-users@gromacs.org

http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to [EMAIL PROTECTED]
.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php




--
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




___
gmx-users mai

Re: [gmx-users] Using user-tables for simulations in vacuum

2008-07-16 Thread sapna sarupria 
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.

Thanks a lot for your help.

Regards
Sapna


On Wed, Jul 16, 2008 at 9:23 AM, David van der Spoel <[EMAIL PROTECTED]>
wrote:

> sapna sarupria wrote:
>
>>
>>
>> -- Forwarded message --
>> From: *sapna sarupria* <[EMAIL PROTECTED] > [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>>
>>
>>
>> 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
>>
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to [EMAIL PROTECTED]
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
> --
> 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
> ___
> gmx-users mailing listgmx-users@gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to [EMAIL PROTECTED]
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>



-- 
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
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Re: [gmx-users] Using user-tables for simulations in vacuum

2008-07-16 Thread David van der Spoel 

sapna sarupria wrote:



-- Forwarded message --
From: *sapna sarupria* <[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 >



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




___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to [EMAIL PROTECTED]

Can't post? Read http://www.gromacs.org/mailing_lists/users.php



--
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
___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
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