Re: [gmx-users] Pressure coupling and cut-off
Dear Justin: Thank you for your suggestions. using shift for vdwtype helps a lot. Can I ask you another question? The density of my system is about 8% larger than the experimental value. Do you have any suggestions on how to reduce the density of the system. Or once the force field and all the parameters are fixed, the density is independent of the MD procedure? I am using NPT ensemble with the mdp I mentioned before with added vdwtype = shift. On Thu, May 14, 2009 at 4:35 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Dear Justin: Thanks for your response. Here is the complete my .mdp file: title = pdm cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 250 ; total 10ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 fourierspacing = 0.20 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in one groups Tcoupl = berendsen tc_grps = PDM tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = PDM ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= PDM tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 The problem you're seeing could be an artifact of the shorter cutoff. Have you tried using DispCorr = EnerPres? Or what about using a Shift function for vdwtype? You might see better energy conservation in that case compared to a plain cutoff. -Justin On Thu, May 14, 2009 at 4:06 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: Yanmei Song wrote: Dear All: I have question about the pressure coupling. I have done a 10ns simulation with 19800 atoms for 120 large molecules using the following pressure coupling. Tcoupl = berendsen tc_grps = PDM tau_t = 0.1 ref_t = 300 Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= PDM tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 Then I did g_energy for the last 3ns and got the results: Energy Average RMSD Fluct. Drift Tot-Drift --- Potential-98061 0 0 0.616681850.04 Temperature 303.561109.602109.602 0.000181791 0.545372 Pressure (bar) 4.48840.811109.8 -0.169835 -509.506 For such a long run the pressure drift is still too much and seem hasn't approached 1bar. Does it mean the system hasn't reach equilibrium yet. I did a similar system by using the same method. it just take 2 or 3ns to reach the equilibrium. and the pressure is around 1.01after the run. The only difference is the cutoff changing from 1.2 to 1.4. Does the cufoff of 1.4 is too large to make the system running slower. Or the pressure coupling method is not working well. Anyone can give me any suggestions? I think it will depend on the interplay of other parameters as well. Posting a complete .mdp file may be more helpful. -Justin --Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department
Re: [gmx-users] Pressure coupling and cut-off
Yanmei Song wrote: Dear Justin: Thank you for your suggestions. using shift for vdwtype helps a lot. Can I ask you another question? The density of my system is about 8% larger than the experimental value. Do you have any suggestions on how to reduce the density of the system. Or once the force field and all the parameters are fixed, the density is independent of the MD procedure? I am using NPT ensemble with the mdp I mentioned before with added vdwtype = shift. Output like density, pressure, energy conservation, etc. are a consequence of both the force field parameters and their proper use. Look into the primary literature for the force field you are using and see how well the parameters are expected to behave. A difference of 8% doesn't sound that unreasonable to me, but the primary literature will be the judge. -Justin On Thu, May 14, 2009 at 4:35 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Yanmei Song wrote: Dear Justin: Thanks for your response. Here is the complete my .mdp file: title = pdm cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 250 ; total 10ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 fourierspacing = 0.20 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in one groups Tcoupl = berendsen tc_grps = PDM tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = PDM ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= PDM tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 The problem you're seeing could be an artifact of the shorter cutoff. Have you tried using DispCorr = EnerPres? Or what about using a Shift function for vdwtype? You might see better energy conservation in that case compared to a plain cutoff. -Justin On Thu, May 14, 2009 at 4:06 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: Yanmei Song wrote: Dear All: I have question about the pressure coupling. I have done a 10ns simulation with 19800 atoms for 120 large molecules using the following pressure coupling. Tcoupl = berendsen tc_grps = PDM tau_t = 0.1 ref_t = 300 Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= PDM tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 Then I did g_energy for the last 3ns and got the results: Energy Average RMSD Fluct. Drift Tot-Drift --- Potential-98061 0 0 0.616681850.04 Temperature 303.561109.602109.602 0.000181791 0.545372 Pressure (bar) 4.48840.811109.8 -0.169835 -509.506 For such a long run the pressure drift is still too much and seem hasn't approached 1bar. Does it mean the system hasn't reach equilibrium yet. I did a similar system by using the same method. it just take 2 or 3ns to reach the equilibrium. and the pressure is around 1.01after the run. The only difference is the cutoff changing from 1.2 to 1.4. Does the cufoff of 1.4 is too large to make the system running slower. Or the pressure
[gmx-users] Pressure coupling and cut-off
Dear All: I have question about the pressure coupling. I have done a 10ns simulation with 19800 atoms for 120 large molecules using the following pressure coupling. Tcoupl = berendsen tc_grps = PDM tau_t = 0.1 ref_t = 300 Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= PDM tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 Then I did g_energy for the last 3ns and got the results: Energy Average RMSD Fluct. Drift Tot-Drift --- Potential-98061 0 00.61668 1850.04 Temperature 303.561109.602109.602 0.000181791 0.545372 Pressure (bar) 4.48840.811109.8 -0.169835 -509.506 For such a long run the pressure drift is still too much and seem hasn't approached 1bar. Does it mean the system hasn't reach equilibrium yet. I did a similar system by using the same method. it just take 2 or 3ns to reach the equilibrium. and the pressure is around 1.01after the run. The only difference is the cutoff changing from 1.2 to 1.4. Does the cufoff of 1.4 is too large to make the system running slower. Or the pressure coupling method is not working well. Anyone can give me any suggestions? -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pressure coupling and cut-off
Yanmei Song wrote: Dear All: I have question about the pressure coupling. I have done a 10ns simulation with 19800 atoms for 120 large molecules using the following pressure coupling. Tcoupl = berendsen tc_grps = PDM tau_t = 0.1 ref_t = 300 Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= PDM tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 Then I did g_energy for the last 3ns and got the results: Energy Average RMSD Fluct. Drift Tot-Drift --- Potential-98061 0 00.61668 1850.04 Temperature 303.561109.602109.602 0.000181791 0.545372 Pressure (bar) 4.48840.811109.8 -0.169835 -509.506 For such a long run the pressure drift is still too much and seem hasn't approached 1bar. Does it mean the system hasn't reach equilibrium yet. I did a similar system by using the same method. it just take 2 or 3ns to reach the equilibrium. and the pressure is around 1.01after the run. The only difference is the cutoff changing from 1.2 to 1.4. Does the cufoff of 1.4 is too large to make the system running slower. Or the pressure coupling method is not working well. Anyone can give me any suggestions? I think it will depend on the interplay of other parameters as well. Posting a complete .mdp file may be more helpful. -Justin -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pressure coupling and cut-off
Dear Justin: Thanks for your response. Here is the complete my .mdp file: title = pdm cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 250 ; total 10ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 fourierspacing = 0.20 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in one groups Tcoupl = berendsen tc_grps = PDM tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = PDM ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= PDM tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 On Thu, May 14, 2009 at 4:06 PM, Justin A. Lemkul jalem...@vt.edu wrote: Yanmei Song wrote: Dear All: I have question about the pressure coupling. I have done a 10ns simulation with 19800 atoms for 120 large molecules using the following pressure coupling. Tcoupl = berendsen tc_grps = PDM tau_t = 0.1 ref_t = 300 Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= PDM tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 Then I did g_energy for the last 3ns and got the results: Energy Average RMSD Fluct. Drift Tot-Drift --- Potential-98061 0 00.61668 1850.04 Temperature 303.561109.602109.602 0.000181791 0.545372 Pressure (bar) 4.48840.811109.8 -0.169835 -509.506 For such a long run the pressure drift is still too much and seem hasn't approached 1bar. Does it mean the system hasn't reach equilibrium yet. I did a similar system by using the same method. it just take 2 or 3ns to reach the equilibrium. and the pressure is around 1.01after the run. The only difference is the cutoff changing from 1.2 to 1.4. Does the cufoff of 1.4 is too large to make the system running slower. Or the pressure coupling method is not working well. Anyone can give me any suggestions? I think it will depend on the interplay of other parameters as well. Posting a complete .mdp file may be more helpful. -Justin -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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://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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Pressure coupling and cut-off
Yanmei Song wrote: Dear Justin: Thanks for your response. Here is the complete my .mdp file: title = pdm cpp = /lib/cpp constraints = all_bonds integrator = md dt = 0.004 ; ps ! nsteps = 250 ; total 10ns. nstcomm = 1 nstxout = 5 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy = 5000 nstxtcout = 25000 nstlist = 10 ns_type = grid pbc = xyz coulombtype = PME rlist = 1.4 rcoulomb= 1.4 rvdw= 1.4 fourierspacing = 0.20 pme_order = 4 ewald_rtol = 1e-5 ; Berendsen temperature coupling is on in one groups Tcoupl = berendsen tc_grps = PDM tau_t = 0.1 ref_t = 300 ; Energy monitoring energygrps = PDM ; Isotropic pressure coupling is now on Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= PDM tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 ; Generate velocites is off at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 10 The problem you're seeing could be an artifact of the shorter cutoff. Have you tried using DispCorr = EnerPres? Or what about using a Shift function for vdwtype? You might see better energy conservation in that case compared to a plain cutoff. -Justin On Thu, May 14, 2009 at 4:06 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: Yanmei Song wrote: Dear All: I have question about the pressure coupling. I have done a 10ns simulation with 19800 atoms for 120 large molecules using the following pressure coupling. Tcoupl = berendsen tc_grps = PDM tau_t = 0.1 ref_t = 300 Pcoupl = berendsen pcoupltype = isotropic ;pc-grps= PDM tau_p = 1.0 ref_p = 1.0 compressibility = 4.5e-5 Then I did g_energy for the last 3ns and got the results: Energy Average RMSD Fluct. Drift Tot-Drift --- Potential-98061 0 0 0.616681850.04 Temperature 303.561109.602109.602 0.000181791 0.545372 Pressure (bar) 4.48840.811109.8 -0.169835 -509.506 For such a long run the pressure drift is still too much and seem hasn't approached 1bar. Does it mean the system hasn't reach equilibrium yet. I did a similar system by using the same method. it just take 2 or 3ns to reach the equilibrium. and the pressure is around 1.01after the run. The only difference is the cutoff changing from 1.2 to 1.4. Does the cufoff of 1.4 is too large to make the system running slower. Or the pressure coupling method is not working well. Anyone can give me any suggestions? I think it will depend on the interplay of other parameters as well. Posting a complete .mdp file may be more helpful. -Justin -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University ___ 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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ___ 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
