Re: [gmx-users] stopped simulation
On 11/6/13 12:53 PM, Ehsan Sadeghi wrote: Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Fatal error: 1 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I used simulated annealing for equilibrating the system in NVT and NPT condition. The mdp files are: NVT -- define = -DPOSRES integrator = md dt = 0.002 ; time step (in ps) nsteps = 25000 ; Maximum number of steps to perform ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 1 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.10.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres ; Pressure coupling is off pcoupl = no ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 300 320 340 360 380 300 320 340 360 380 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= no constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 - NPT define = -DPOSRES integrator = md dt = 0.002 nsteps = 25000 ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstfout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 5 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.10.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 380 360 340 320 300 380 360 340 320 300 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= no ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= yes ;continuation from NVT constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 -- Is the equilibration time is long enough? I appreciate any help/suggestion regarding my case. The cutoffs values (1.5) are wrong for using any of the Gromos parameter sets. Likely the dynamics have become unstable due to violation of the physical model. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] stopped simulation
Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I right? Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 6, 2013 10:54:42 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 12:53 PM, Ehsan Sadeghi wrote: Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Fatal error: 1 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I used simulated annealing for equilibrating the system in NVT and NPT condition. The mdp files are: NVT -- define = -DPOSRES integrator = md dt = 0.002 ; time step (in ps) nsteps = 25000 ; Maximum number of steps to perform ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 1 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.10.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres ; Pressure coupling is off pcoupl = no ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 300 320 340 360 380 300 320 340 360 380 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= no constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 - NPT define = -DPOSRES integrator = md dt = 0.002 nsteps = 25000 ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstfout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 5 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.10.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 380 360 340 320 300 380 360 340 320 300 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= no ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= yes ;continuation from NVT constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 -- Is the equilibration time is long enough? I appreciate any help/suggestion regarding my case. The cutoffs values (1.5) are wrong for using any of the Gromos parameter sets. Likely the dynamics have become unstable due to violation of the physical model. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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
Re: [gmx-users] stopped simulation
On 11/6/13 2:14 PM, Ehsan Sadeghi wrote: Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I right? No. The cutoff value is not a function of box size; it is a fixed property of the force field. No wonder the simulation is crashing. If your box is only 0.5 nm, then a cutoff of 1.5 nm is triple-counting interactions across PBC! Refer to the primary literature for the Gromos parameter set you are using for proper settings. You haven't said which one you're using, and there may be slight differences between them. If the value you're using isn't taken directly from a paper, it's not credible. -Justin Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 6, 2013 10:54:42 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 12:53 PM, Ehsan Sadeghi wrote: Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Fatal error: 1 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I used simulated annealing for equilibrating the system in NVT and NPT condition. The mdp files are: NVT -- define = -DPOSRES integrator = md dt = 0.002 ; time step (in ps) nsteps = 25000 ; Maximum number of steps to perform ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 1 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres ; Pressure coupling is off pcoupl = no ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 300 320 340 360 380 300 320 340 360 380 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= no constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 - NPT define = -DPOSRES integrator = md dt = 0.002 nsteps = 25000 ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstfout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 5 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 380 360 340 320 300 380 360 340 320 300 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= no ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= yes ;continuation from NVT constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 -- Is the equilibration time is long enough? I appreciate any help/suggestion regarding my case. The cutoffs values (1.5) are wrong for using any of the Gromos parameter sets. Likely the dynamics have become unstable due to violation of the physical model. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences
Re: [gmx-users] stopped simulation
What is this cut-off radius mentioned in the manual? The cut-off radius used to truncate non-bonded inter-actions may not exceed half the shortest box vector. Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 6, 2013 11:22:09 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 2:14 PM, Ehsan Sadeghi wrote: Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I right? No. The cutoff value is not a function of box size; it is a fixed property of the force field. No wonder the simulation is crashing. If your box is only 0.5 nm, then a cutoff of 1.5 nm is triple-counting interactions across PBC! Refer to the primary literature for the Gromos parameter set you are using for proper settings. You haven't said which one you're using, and there may be slight differences between them. If the value you're using isn't taken directly from a paper, it's not credible. -Justin Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 6, 2013 10:54:42 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 12:53 PM, Ehsan Sadeghi wrote: Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Fatal error: 1 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I used simulated annealing for equilibrating the system in NVT and NPT condition. The mdp files are: NVT -- define = -DPOSRES integrator = md dt = 0.002 ; time step (in ps) nsteps = 25000 ; Maximum number of steps to perform ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 1 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres ; Pressure coupling is off pcoupl = no ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 300 320 340 360 380 300 320 340 360 380 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= no constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 - NPT define = -DPOSRES integrator = md dt = 0.002 nsteps = 25000 ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstfout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 5 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 380 360 340 320 300 380 360 340 320 300 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= no ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= yes ;continuation from NVT constraint_algorithm = lincs
Re: [gmx-users] stopped simulation
On 11/6/13 2:27 PM, Ehsan Sadeghi wrote: What is this cut-off radius mentioned in the manual? The cut-off radius used to truncate non-bonded inter-actions may not exceed half the shortest box vector. It refers to the longest cutoff used to evaluate nonbonded interactions, whatever that may be for your chosen force field. http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Convention -Justin Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 6, 2013 11:22:09 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 2:14 PM, Ehsan Sadeghi wrote: Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I right? No. The cutoff value is not a function of box size; it is a fixed property of the force field. No wonder the simulation is crashing. If your box is only 0.5 nm, then a cutoff of 1.5 nm is triple-counting interactions across PBC! Refer to the primary literature for the Gromos parameter set you are using for proper settings. You haven't said which one you're using, and there may be slight differences between them. If the value you're using isn't taken directly from a paper, it's not credible. -Justin Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 6, 2013 10:54:42 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 12:53 PM, Ehsan Sadeghi wrote: Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Fatal error: 1 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I used simulated annealing for equilibrating the system in NVT and NPT condition. The mdp files are: NVT -- define = -DPOSRES integrator = md dt = 0.002 ; time step (in ps) nsteps = 25000 ; Maximum number of steps to perform ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 1 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres ; Pressure coupling is off pcoupl = no ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 300 320 340 360 380 300 320 340 360 380 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= no constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 - NPT define = -DPOSRES integrator = md dt = 0.002 nsteps = 25000 ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstfout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 5 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 380 360 340 320 300 380 360 340 320
Re: [gmx-users] stopped simulation
On Wed, Nov 6, 2013 at 8:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/6/13 2:14 PM, Ehsan Sadeghi wrote: Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I right? No. The cutoff value is not a function of box size; it is a fixed property of the force field. No wonder the simulation is crashing. If your box is only 0.5 nm, then a cutoff of 1.5 nm is triple-counting interactions across PBC! Triple counting is not possible, per minimum-image convention. I think Ehsan's report of a 0.5nm box size is probably wrong, e.g. per its documentation, editconf -d 0.5 does not produce a 0.5nm box. Mark Refer to the primary literature for the Gromos parameter set you are using for proper settings. You haven't said which one you're using, and there may be slight differences between them. If the value you're using isn't taken directly from a paper, it's not credible. -Justin Cheers, Ehsan - Original Message - From: Justin Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-users@gromacs.org Sent: Wednesday, November 6, 2013 10:54:42 AM Subject: Re: [gmx-users] stopped simulation On 11/6/13 12:53 PM, Ehsan Sadeghi wrote: Hi gmx users, I have simulated ionomer in water solution using gromos force field. But in middle of simulation(after 2 ns) the simulation stopped and I received these messages: WARNING: Listed nonbonded interaction between particles 174 and 188 at distance 3f which is larger than the table limit 3f nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Fatal error: 1 particles communicated to PME node 5 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y. This usually means that your system is not well equilibrated. I used simulated annealing for equilibrating the system in NVT and NPT condition. The mdp files are: NVT -- define = -DPOSRES integrator = md dt = 0.002 ; time step (in ps) nsteps = 25000 ; Maximum number of steps to perform ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 1 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres ; Pressure coupling is off pcoupl = no ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 300 320 340 360 380 300 320 340 360 380 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= yes gen_temp = 300 gen_seed = -1 ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= no constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 - NPT define = -DPOSRES integrator = md dt = 0.002 nsteps = 25000 ; OUTPUT CONTROL OPTIONS nstxout= 500 nstvout= 500 nstfout= 500 nstenergy = 500 nstlog = 500 energygrps = Non-Water Water ; NEIGHBORSEARCHING PARAMETERS nstlist= 5 ns_type= grid rlist = 1.5 pbc= xyz ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype= PME pme_order = 4 fourierspacing= 0.16 rcoulomb = 1.5 vdw-type = Cut-off rvdw = 1.5 ; Temperature coupling tcoupl = v-rescale tc-grps= Non-Water Water tau_t = 0.1 0.1 ref_t = 300300 ; Dispersion correction DispCorr = EnerPres pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau_p = 2.0 compressibility = 4.5e-5 ref_p = 1.0 refcoord_scaling = com ; Annealing annealing = single single annealing-npoints = 5 5 annealing-time = 0 10 20 30 40 0 10 20 30 40 annealing-temp = 380 360 340 320 300 380 360 340 320 300 ; GENERATE VELOCITIES FOR STARTUP RUN gen_vel= no ; OPTIONS FOR BONDS constraints = ; all-bonds continuation= yes ;continuation from NVT constraint_algorithm = lincs lincs_iter = 1 lincs_order= 4 -- Is the equilibration time is long enough
Re: [gmx-users] stopped simulation
On 11/6/13 4:52 PM, Mark Abraham wrote: On Wed, Nov 6, 2013 at 8:22 PM, Justin Lemkul jalem...@vt.edu wrote: On 11/6/13 2:14 PM, Ehsan Sadeghi wrote: Many thanks Justin. What is an appropriate cut-off value? My box size is d= 0.5 nm; based on the definition of cut-off radius, its value shouble be smaller than d/2; therefore 0.24 is an appropriate cut-off value. Am I right? No. The cutoff value is not a function of box size; it is a fixed property of the force field. No wonder the simulation is crashing. If your box is only 0.5 nm, then a cutoff of 1.5 nm is triple-counting interactions across PBC! Triple counting is not possible, per minimum-image convention. I think True. Thinking too quickly ;) Ehsan's report of a 0.5nm box size is probably wrong, e.g. per its documentation, editconf -d 0.5 does not produce a 0.5nm box. editconf -box 0.5 does produce such a box, though, so it is possible. grompp should have warned quite obviously about the combination of a 0.5-nm box with 1.5-nm cutoffs, though. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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
