Re: [gmx-users] Using user-tables for simulations in vacuum
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.
Re: [gmx-users] Using user-tables for simulations in vacuum
sapna sarupria wrote: -- Forwarded message -- From: *sapna sarupria* [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 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
Re: [gmx-users] Using user-tables for simulations in vacuum
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] 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 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
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] wrote: sapna sarupria wrote: -- Forwarded message -- From: *sapna sarupria* [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 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 mailto:gmx-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] mailto:[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] mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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] mailto:[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
Re: [gmx-users] Using user-tables for simulations in vacuum
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] mailto:[EMAIL PROTECTED] wrote: sapna sarupria wrote: -- Forwarded message -- From: *sapna sarupria* [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 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 mailto:gmx-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] mailto:[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] mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] mailto:[EMAIL PROTECTED] http://folding.bmc.uu.se
[gmx-users] Using user-tables for simulations in vacuum
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. Thank you Regards Sapna ___ 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
