Re: [gmx-users] LINCS warning and segmentation fault for methane in 1-octanol simulation
vivek sharma wrote: Hi There, I was trying to run a equilibrium run (npt) for system of Methane in 1-octanol (1 methane molecule with 200 1-octanol molecules with OPLS FF parameters). Following is the series of steps I followed: 1. Energy minimization with steep integrator for 5000 steps 2. Energy minimization with l-bfgs integrator for 5000 steps 3. NVT run for 100 ps with sd integrator 4. NPT run for 100 ps with sd integrator (with Pcoupl = Parrinello-Rahman, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) During the NPT run I am ending up with following error (too many LINCS warning): - Step 25406, time 50.812 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 11.778495, max 363.475445 (between atoms 2158 and 2157) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2152 2150 90.00.1090 1.3690 0.1090 2152 2151 90.00.1090 36.5266 0.1090 2158 2156 90.00.1091 0.5637 0.1090 2158 2157 90.00.2349 39.7278 0.1090 Back Off! I just backed up step25406b_n0.pdb to ./#step25406b_n0.pdb.1# Back Off! I just backed up step25406c_n0.pdb to ./#step25406c_n0.pdb.1# Wrote pdb files with previous and current coordinates Segmentation fault *.mdp files for above simulation are adapted from tutorial on free energy calculation by Justin. Please suggest me what could be wrong with above simulation. The answer for LINCS warnings is always the same - the system has become unstable due to inappropriate geometry, bad .mdp settings, or a combination of both. To troubleshoot, start by turning off the free energy code to make sure your system is actually stable. If it's not, refer here: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System If it is stable, turn back on whatever free energy settings you're using. I assume, based on the tutorial, that this is a simple vdW transformation? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS warning and segmentation fault for methane in 1-octanol simulation
Hi Justin, Thanks for your response. After posting my query, I tried running the similar set with NPT run for 100 ps with sd integrator (with Pcoupl = berensen, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) On giving berendsen instead of Parrinello-Rahman for pressure coupling, job finished successfully. Can you comment on this? As par the tutorial I am using simple vdW transformation only as mentioned below - couple-moltype = Methane ; name of moleculetype to decouple couple-lambda0 = vdw ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW - Thanks, Vivek On 09/02/2012, Justin A. Lemkul jalem...@vt.edu wrote: vivek sharma wrote: Hi There, I was trying to run a equilibrium run (npt) for system of Methane in 1-octanol (1 methane molecule with 200 1-octanol molecules with OPLS FF parameters). Following is the series of steps I followed: 1. Energy minimization with steep integrator for 5000 steps 2. Energy minimization with l-bfgs integrator for 5000 steps 3. NVT run for 100 ps with sd integrator 4. NPT run for 100 ps with sd integrator (with Pcoupl = Parrinello-Rahman, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) During the NPT run I am ending up with following error (too many LINCS warning): - Step 25406, time 50.812 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 11.778495, max 363.475445 (between atoms 2158 and 2157) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2152 2150 90.00.1090 1.3690 0.1090 2152 2151 90.00.1090 36.5266 0.1090 2158 2156 90.00.1091 0.5637 0.1090 2158 2157 90.00.2349 39.7278 0.1090 Back Off! I just backed up step25406b_n0.pdb to ./#step25406b_n0.pdb.1# Back Off! I just backed up step25406c_n0.pdb to ./#step25406c_n0.pdb.1# Wrote pdb files with previous and current coordinates Segmentation fault *.mdp files for above simulation are adapted from tutorial on free energy calculation by Justin. Please suggest me what could be wrong with above simulation. The answer for LINCS warnings is always the same - the system has become unstable due to inappropriate geometry, bad .mdp settings, or a combination of both. To troubleshoot, start by turning off the free energy code to make sure your system is actually stable. If it's not, refer here: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System If it is stable, turn back on whatever free energy settings you're using. I assume, based on the tutorial, that this is a simple vdW transformation? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] LINCS warning and segmentation fault for methane in 1-octanol simulation
On 10/02/2012 4:41 PM, vivek sharma wrote: Hi Justin, Thanks for your response. After posting my query, I tried running the similar set with NPT run for 100 ps with sd integrator (with Pcoupl = berensen, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) On giving berendsen instead of Parrinello-Rahman for pressure coupling, job finished successfully. Can you comment on this? I suggest you read the manual section on pressure coupling, which likely explains this observation. Mark As par the tutorial I am using simple vdW transformation only as mentioned below - couple-moltype = Methane ; name of moleculetype to decouple couple-lambda0 = vdw ; only van der Waals interactions couple-lambda1 = none ; turn off everything, in this case only vdW - Thanks, Vivek On 09/02/2012, Justin A. Lemkuljalem...@vt.edu wrote: vivek sharma wrote: Hi There, I was trying to run a equilibrium run (npt) for system of Methane in 1-octanol (1 methane molecule with 200 1-octanol molecules with OPLS FF parameters). Following is the series of steps I followed: 1. Energy minimization with steep integrator for 5000 steps 2. Energy minimization with l-bfgs integrator for 5000 steps 3. NVT run for 100 ps with sd integrator 4. NPT run for 100 ps with sd integrator (with Pcoupl = Parrinello-Rahman, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) During the NPT run I am ending up with following error (too many LINCS warning): - Step 25406, time 50.812 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 11.778495, max 363.475445 (between atoms 2158 and 2157) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2152 2150 90.00.1090 1.3690 0.1090 2152 2151 90.00.1090 36.5266 0.1090 2158 2156 90.00.1091 0.5637 0.1090 2158 2157 90.00.2349 39.7278 0.1090 Back Off! I just backed up step25406b_n0.pdb to ./#step25406b_n0.pdb.1# Back Off! I just backed up step25406c_n0.pdb to ./#step25406c_n0.pdb.1# Wrote pdb files with previous and current coordinates Segmentation fault *.mdp files for above simulation are adapted from tutorial on free energy calculation by Justin. Please suggest me what could be wrong with above simulation. The answer for LINCS warnings is always the same - the system has become unstable due to inappropriate geometry, bad .mdp settings, or a combination of both. To troubleshoot, start by turning off the free energy code to make sure your system is actually stable. If it's not, refer here: http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System If it is stable, turn back on whatever free energy settings you're using. I assume, based on the tutorial, that this is a simple vdW transformation? -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] LINCS warning and segmentation fault for methane in 1-octanol simulation
Hi There, I was trying to run a equilibrium run (npt) for system of Methane in 1-octanol (1 methane molecule with 200 1-octanol molecules with OPLS FF parameters). Following is the series of steps I followed: 1. Energy minimization with steep integrator for 5000 steps 2. Energy minimization with l-bfgs integrator for 5000 steps 3. NVT run for 100 ps with sd integrator 4. NPT run for 100 ps with sd integrator (with Pcoupl = Parrinello-Rahman, tau_p = 0.5, compressibility = 4.5e-05, ref_p = 1.0) During the NPT run I am ending up with following error (too many LINCS warning): - Step 25406, time 50.812 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 11.778495, max 363.475445 (between atoms 2158 and 2157) bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 2152 2150 90.00.1090 1.3690 0.1090 2152 2151 90.00.1090 36.5266 0.1090 2158 2156 90.00.1091 0.5637 0.1090 2158 2157 90.00.2349 39.7278 0.1090 Back Off! I just backed up step25406b_n0.pdb to ./#step25406b_n0.pdb.1# Back Off! I just backed up step25406c_n0.pdb to ./#step25406c_n0.pdb.1# Wrote pdb files with previous and current coordinates Segmentation fault *.mdp files for above simulation are adapted from tutorial on free energy calculation by Justin. Please suggest me what could be wrong with above simulation. Regards, Vivek Sharma -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
