Re: [gmx-users] Gromos 53a6, .mdp parameters for reaction field
As an update, After reading the suggested links I tried two .mdp files which were suggested in discussions as solutions. Both worked without any problem on my system. 1) rlist/r(columb/vdw)=(1.4/1.4) , in fact the problem seems to be the twin-range + RF 2) I used twin-range + RF BUT I reduced the nstlist to 1, this also works for my system. Thanks for your comments. Cheers Mohsen On Tue, Jul 21, 2015 at 4:44 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: I looked at the first link, it was a useful discussion. Now, I am trying suggestions with rlist/r(columb/vdw)=(1.4/1.4) and everything is working properly till now. It seems the problem was the twin-range + RF with this version of Gromacs as has been discussed and you mentioned already. I am playing a little bit to see if I everything will be fine with the rest of test simulation. I will reply again after my tests. Thanks for the links Cheers Mohsen On Tue, Jul 21, 2015 at 4:21 PM, João M. Damas jmda...@itqb.unl.pt wrote: I really think you may be losing time with LINCS parameters. Look at these links too: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-March/088108.html http://redmine.gromacs.org/issues/1400 You use a twin-range, i.e. a rlist/r(coulomb/vdw) of 0.8/1.4, so I really think that this may be the source of your problems. The links that I sent you present solutions to your problem, but almost always at a computational cost, i.e. slower simulations. João On Tue, Jul 21, 2015 at 9:34 PM, V.V.Chaban vvcha...@gmail.com wrote: Maybe indeed downgrade to an earlier version. I, for sure, successfully used reaction field with gromacs 3-3-3 (imagine when it was). Professor Vitaly V. Chaban On Tue, Jul 21, 2015 at 4:49 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Hi Chaban, Me too, but I do not know why starting with the same initial structures and also starting from equilibrated structures again cause LINCS problems in one not in the other one. I have tried lincs-iter and lincs-order and also lincs allowable angle deviations but LINCS error still exist. This is why I think there is something wrong with other parameters, e.g. reaction field! Sure, I will look at epsilon_r, thanks. On Tue, Jul 21, 2015 at 11:44 AM, V.V.Chaban vvcha...@gmail.com wrote: I do not see much connection between bond constraints and treatment of electrostatics beyond the cut-off distance. There is also an epsilon_r keyword. I would investigate what exactly it means and whether it is used in the reaction field procedure. The all-bonds contraint often results in different problems. You will have to play with the relevant parameters, like lincs_order and allowable deviation. On Tue, Jul 21, 2015 at 2:28 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Gromacs users, I am interested in simulation of lipid bilayers with Gromos96 53a6. As I understood this force field has been parametrized with reaction field instead of pme. Based on literatures, I have the following .mdp parameters: But I am not sure of those as my system has lots of LINCS warnings with these parameters. integrator = md tinit = 0 dt = 0.002 nsteps = 5 nstcomm = 1 comm-grps= nstxout = 0 nstvout = 0 nstfout = 0 nstenergy= 100 nstxtcout= 5000 xtc-precision = 1000 energygrps = system nstlist = 5 ns_type = grid pbc = xyz rlist = 0.8 coulombtype = reaction_field rcoulomb-switch= 0 rcoulomb = 1.4 epsilon_rf = 62 vdw-type = Cut-off rvdw-switch = 0 rvdw= 1.4 DispCorr = no tcoupl = v-rescale tc_grps = lipid water_ion tau_t =0.1 0.1 ref_t =353 353 Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.6e-5 4.6e-5 ref_p = 1.0 1.0 gen_vel= yes gen_temp = 353 gen_seed = 17352 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no shake-tol= 1e-04 morse= no Interestingly, when I use common Gromos
Re: [gmx-users] Gromos 53a6, .mdp parameters for reaction field
Hi Mohsen, I am struggling with the same problem would you mind if I ask you to send me your .mdp file ? Cheers James On Tue, Aug 11, 2015 at 4:00 AM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: As an update, After reading the suggested links I tried two .mdp files which were suggested in discussions as solutions. Both worked without any problem on my system. 1) rlist/r(columb/vdw)=(1.4/1.4) , in fact the problem seems to be the twin-range + RF 2) I used twin-range + RF BUT I reduced the nstlist to 1, this also works for my system. Thanks for your comments. Cheers Mohsen On Tue, Jul 21, 2015 at 4:44 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: I looked at the first link, it was a useful discussion. Now, I am trying suggestions with rlist/r(columb/vdw)=(1.4/1.4) and everything is working properly till now. It seems the problem was the twin-range + RF with this version of Gromacs as has been discussed and you mentioned already. I am playing a little bit to see if I everything will be fine with the rest of test simulation. I will reply again after my tests. Thanks for the links Cheers Mohsen On Tue, Jul 21, 2015 at 4:21 PM, João M. Damas jmda...@itqb.unl.pt wrote: I really think you may be losing time with LINCS parameters. Look at these links too: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-March/088108.html http://redmine.gromacs.org/issues/1400 You use a twin-range, i.e. a rlist/r(coulomb/vdw) of 0.8/1.4, so I really think that this may be the source of your problems. The links that I sent you present solutions to your problem, but almost always at a computational cost, i.e. slower simulations. João On Tue, Jul 21, 2015 at 9:34 PM, V.V.Chaban vvcha...@gmail.com wrote: Maybe indeed downgrade to an earlier version. I, for sure, successfully used reaction field with gromacs 3-3-3 (imagine when it was). Professor Vitaly V. Chaban On Tue, Jul 21, 2015 at 4:49 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Hi Chaban, Me too, but I do not know why starting with the same initial structures and also starting from equilibrated structures again cause LINCS problems in one not in the other one. I have tried lincs-iter and lincs-order and also lincs allowable angle deviations but LINCS error still exist. This is why I think there is something wrong with other parameters, e.g. reaction field! Sure, I will look at epsilon_r, thanks. On Tue, Jul 21, 2015 at 11:44 AM, V.V.Chaban vvcha...@gmail.com wrote: I do not see much connection between bond constraints and treatment of electrostatics beyond the cut-off distance. There is also an epsilon_r keyword. I would investigate what exactly it means and whether it is used in the reaction field procedure. The all-bonds contraint often results in different problems. You will have to play with the relevant parameters, like lincs_order and allowable deviation. On Tue, Jul 21, 2015 at 2:28 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Gromacs users, I am interested in simulation of lipid bilayers with Gromos96 53a6. As I understood this force field has been parametrized with reaction field instead of pme. Based on literatures, I have the following .mdp parameters: But I am not sure of those as my system has lots of LINCS warnings with these parameters. integrator = md tinit = 0 dt = 0.002 nsteps = 5 nstcomm = 1 comm-grps= nstxout = 0 nstvout = 0 nstfout = 0 nstenergy= 100 nstxtcout= 5000 xtc-precision = 1000 energygrps = system nstlist = 5 ns_type = grid pbc = xyz rlist = 0.8 coulombtype = reaction_field rcoulomb-switch= 0 rcoulomb = 1.4 epsilon_rf = 62 vdw-type = Cut-off rvdw-switch = 0 rvdw= 1.4 DispCorr = no tcoupl = v-rescale tc_grps = lipid water_ion tau_t =0.1 0.1 ref_t =353 353 Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.6e-5 4.6e-5 ref_p = 1.0
[gmx-users] Gromos 53a6, .mdp parameters for reaction field
Dear Gromacs users, I am interested in simulation of lipid bilayers with Gromos96 53a6. As I understood this force field has been parametrized with reaction field instead of pme. Based on literatures, I have the following .mdp parameters: But I am not sure of those as my system has lots of LINCS warnings with these parameters. integrator = md tinit = 0 dt = 0.002 nsteps = 5 nstcomm = 1 comm-grps= nstxout = 0 nstvout = 0 nstfout = 0 nstenergy= 100 nstxtcout= 5000 xtc-precision = 1000 energygrps = system nstlist = 5 ns_type = grid pbc = xyz rlist = 0.8 coulombtype = reaction_field rcoulomb-switch= 0 rcoulomb = 1.4 epsilon_rf = 62 vdw-type = Cut-off rvdw-switch = 0 rvdw= 1.4 DispCorr = no tcoupl = v-rescale tc_grps = lipid water_ion tau_t =0.1 0.1 ref_t =353 353 Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.6e-5 4.6e-5 ref_p = 1.0 1.0 gen_vel= yes gen_temp = 353 gen_seed = 17352 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no shake-tol= 1e-04 morse= no Interestingly, when I use common Gromos parameters including pme, as follows, I do not have any LINCS problem with my system. integrator= md tinit= 0 dt = 0.002 nsteps = 5 pbc= xyz comm-mode = linear nstcomm= 1 comm-grps = system nstxout = 0 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid nstenergy = 100 nstxtcout = 5000 energygrps= system coulombtype = pme rcoulomb= 1.0 rlist= 1.0 vdw-type= cutoff rvdw = 1.0 DispCorr = no table-extension = 1 tcoupl = v-rescale tc-grps= lipid water_ion tau-t = 0.1 0.1 ref-t= 353 353 Pcoupl= berendsen Pcoupltype = semiisotropic ref-p= 1.0 1.0 tau-p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 constraints = all-bonds constraint-algorithm = Lincs gen_vel= yes gen_temp= 353 gen_seed= -1 Since the initial structures are the same, I think my parameters for reaction field one has problem. I have also tried shorter time steps (even 0.5 fs) and also started from different initial structures but the problem still exist. I searched the mailing list but I could not find my answer completely. Please let me know if you have any idea about parameters or if you have any .mdp file for reaction field (Gromos 53a6). Cheers Mohsen -- *Rewards work better than punishment ...* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromos 53a6, .mdp parameters for reaction field
I do not see much connection between bond constraints and treatment of electrostatics beyond the cut-off distance. There is also an epsilon_r keyword. I would investigate what exactly it means and whether it is used in the reaction field procedure. The all-bonds contraint often results in different problems. You will have to play with the relevant parameters, like lincs_order and allowable deviation. On Tue, Jul 21, 2015 at 2:28 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Gromacs users, I am interested in simulation of lipid bilayers with Gromos96 53a6. As I understood this force field has been parametrized with reaction field instead of pme. Based on literatures, I have the following .mdp parameters: But I am not sure of those as my system has lots of LINCS warnings with these parameters. integrator = md tinit = 0 dt = 0.002 nsteps = 5 nstcomm = 1 comm-grps= nstxout = 0 nstvout = 0 nstfout = 0 nstenergy= 100 nstxtcout= 5000 xtc-precision = 1000 energygrps = system nstlist = 5 ns_type = grid pbc = xyz rlist = 0.8 coulombtype = reaction_field rcoulomb-switch= 0 rcoulomb = 1.4 epsilon_rf = 62 vdw-type = Cut-off rvdw-switch = 0 rvdw= 1.4 DispCorr = no tcoupl = v-rescale tc_grps = lipid water_ion tau_t =0.1 0.1 ref_t =353 353 Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.6e-5 4.6e-5 ref_p = 1.0 1.0 gen_vel= yes gen_temp = 353 gen_seed = 17352 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no shake-tol= 1e-04 morse= no Interestingly, when I use common Gromos parameters including pme, as follows, I do not have any LINCS problem with my system. integrator= md tinit= 0 dt = 0.002 nsteps = 5 pbc= xyz comm-mode = linear nstcomm= 1 comm-grps = system nstxout = 0 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid nstenergy = 100 nstxtcout = 5000 energygrps= system coulombtype = pme rcoulomb= 1.0 rlist= 1.0 vdw-type= cutoff rvdw = 1.0 DispCorr = no table-extension = 1 tcoupl = v-rescale tc-grps= lipid water_ion tau-t = 0.1 0.1 ref-t= 353 353 Pcoupl= berendsen Pcoupltype = semiisotropic ref-p= 1.0 1.0 tau-p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 constraints = all-bonds constraint-algorithm = Lincs gen_vel= yes gen_temp= 353 gen_seed= -1 Since the initial structures are the same, I think my parameters for reaction field one has problem. I have also tried shorter time steps (even 0.5 fs) and also started from different initial structures but the problem still exist. I searched the mailing list but I could not find my answer completely. Please let me know if you have any idea about parameters or if you have any .mdp file for reaction field (Gromos 53a6). Cheers Mohsen -- *Rewards work better than punishment ...* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromos 53a6, .mdp parameters for reaction field
Hi Joao, Thanks for comment, I am using 4.6.7 version. On Tue, Jul 21, 2015 at 12:09 PM, João M. Damas jmda...@itqb.unl.pt wrote: I have not looked thoroughly to your parameters, but which version of GROMACS are you using? Any version from 4.5.X onwards is known to be problematic with reaction field and twin-range (and I believe it has not been solved). It's hard to follow the entire conversation, but check here for part of it: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2011-November/005435.html João On Tue, Jul 21, 2015 at 6:44 PM, V.V.Chaban vvcha...@gmail.com wrote: I do not see much connection between bond constraints and treatment of electrostatics beyond the cut-off distance. There is also an epsilon_r keyword. I would investigate what exactly it means and whether it is used in the reaction field procedure. The all-bonds contraint often results in different problems. You will have to play with the relevant parameters, like lincs_order and allowable deviation. On Tue, Jul 21, 2015 at 2:28 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Gromacs users, I am interested in simulation of lipid bilayers with Gromos96 53a6. As I understood this force field has been parametrized with reaction field instead of pme. Based on literatures, I have the following .mdp parameters: But I am not sure of those as my system has lots of LINCS warnings with these parameters. integrator = md tinit = 0 dt = 0.002 nsteps = 5 nstcomm = 1 comm-grps= nstxout = 0 nstvout = 0 nstfout = 0 nstenergy= 100 nstxtcout= 5000 xtc-precision = 1000 energygrps = system nstlist = 5 ns_type = grid pbc = xyz rlist = 0.8 coulombtype = reaction_field rcoulomb-switch= 0 rcoulomb = 1.4 epsilon_rf = 62 vdw-type = Cut-off rvdw-switch = 0 rvdw= 1.4 DispCorr = no tcoupl = v-rescale tc_grps = lipid water_ion tau_t =0.1 0.1 ref_t =353 353 Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.6e-5 4.6e-5 ref_p = 1.0 1.0 gen_vel= yes gen_temp = 353 gen_seed = 17352 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no shake-tol= 1e-04 morse= no Interestingly, when I use common Gromos parameters including pme, as follows, I do not have any LINCS problem with my system. integrator= md tinit= 0 dt = 0.002 nsteps = 5 pbc= xyz comm-mode = linear nstcomm= 1 comm-grps = system nstxout = 0 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid nstenergy = 100 nstxtcout = 5000 energygrps= system coulombtype = pme rcoulomb= 1.0 rlist= 1.0 vdw-type= cutoff rvdw = 1.0 DispCorr = no table-extension = 1 tcoupl = v-rescale tc-grps= lipid water_ion tau-t = 0.1 0.1 ref-t= 353 353 Pcoupl= berendsen Pcoupltype = semiisotropic ref-p= 1.0 1.0 tau-p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 constraints = all-bonds constraint-algorithm = Lincs gen_vel= yes gen_temp= 353 gen_seed= -1 Since the initial structures are the same, I think my parameters for reaction field one has problem. I have also tried shorter time steps (even 0.5 fs) and also started from different initial structures but the problem still exist. I searched the mailing list but I could not find my answer completely. Please let me know if you have any idea about parameters or if you have any
Re: [gmx-users] Gromos 53a6, .mdp parameters for reaction field
Hi Chaban, Me too, but I do not know why starting with the same initial structures and also starting from equilibrated structures again cause LINCS problems in one not in the other one. I have tried lincs-iter and lincs-order and also lincs allowable angle deviations but LINCS error still exist. This is why I think there is something wrong with other parameters, e.g. reaction field! Sure, I will look at epsilon_r, thanks. On Tue, Jul 21, 2015 at 11:44 AM, V.V.Chaban vvcha...@gmail.com wrote: I do not see much connection between bond constraints and treatment of electrostatics beyond the cut-off distance. There is also an epsilon_r keyword. I would investigate what exactly it means and whether it is used in the reaction field procedure. The all-bonds contraint often results in different problems. You will have to play with the relevant parameters, like lincs_order and allowable deviation. On Tue, Jul 21, 2015 at 2:28 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Gromacs users, I am interested in simulation of lipid bilayers with Gromos96 53a6. As I understood this force field has been parametrized with reaction field instead of pme. Based on literatures, I have the following .mdp parameters: But I am not sure of those as my system has lots of LINCS warnings with these parameters. integrator = md tinit = 0 dt = 0.002 nsteps = 5 nstcomm = 1 comm-grps= nstxout = 0 nstvout = 0 nstfout = 0 nstenergy= 100 nstxtcout= 5000 xtc-precision = 1000 energygrps = system nstlist = 5 ns_type = grid pbc = xyz rlist = 0.8 coulombtype = reaction_field rcoulomb-switch= 0 rcoulomb = 1.4 epsilon_rf = 62 vdw-type = Cut-off rvdw-switch = 0 rvdw= 1.4 DispCorr = no tcoupl = v-rescale tc_grps = lipid water_ion tau_t =0.1 0.1 ref_t =353 353 Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.6e-5 4.6e-5 ref_p = 1.0 1.0 gen_vel= yes gen_temp = 353 gen_seed = 17352 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no shake-tol= 1e-04 morse= no Interestingly, when I use common Gromos parameters including pme, as follows, I do not have any LINCS problem with my system. integrator= md tinit= 0 dt = 0.002 nsteps = 5 pbc= xyz comm-mode = linear nstcomm= 1 comm-grps = system nstxout = 0 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid nstenergy = 100 nstxtcout = 5000 energygrps= system coulombtype = pme rcoulomb= 1.0 rlist= 1.0 vdw-type= cutoff rvdw = 1.0 DispCorr = no table-extension = 1 tcoupl = v-rescale tc-grps= lipid water_ion tau-t = 0.1 0.1 ref-t= 353 353 Pcoupl= berendsen Pcoupltype = semiisotropic ref-p= 1.0 1.0 tau-p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 constraints = all-bonds constraint-algorithm = Lincs gen_vel= yes gen_temp= 353 gen_seed= -1 Since the initial structures are the same, I think my parameters for reaction field one has problem. I have also tried shorter time steps (even 0.5 fs) and also started from different initial structures but the problem still exist. I searched the mailing list but I could not find my answer completely. Please let me know if you have any idea about parameters or if you have any .mdp file for reaction field (Gromos 53a6). Cheers Mohsen -- *Rewards work better than punishment ...* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
Re: [gmx-users] Gromos 53a6, .mdp parameters for reaction field
Maybe indeed downgrade to an earlier version. I, for sure, successfully used reaction field with gromacs 3-3-3 (imagine when it was). Professor Vitaly V. Chaban On Tue, Jul 21, 2015 at 4:49 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Hi Chaban, Me too, but I do not know why starting with the same initial structures and also starting from equilibrated structures again cause LINCS problems in one not in the other one. I have tried lincs-iter and lincs-order and also lincs allowable angle deviations but LINCS error still exist. This is why I think there is something wrong with other parameters, e.g. reaction field! Sure, I will look at epsilon_r, thanks. On Tue, Jul 21, 2015 at 11:44 AM, V.V.Chaban vvcha...@gmail.com wrote: I do not see much connection between bond constraints and treatment of electrostatics beyond the cut-off distance. There is also an epsilon_r keyword. I would investigate what exactly it means and whether it is used in the reaction field procedure. The all-bonds contraint often results in different problems. You will have to play with the relevant parameters, like lincs_order and allowable deviation. On Tue, Jul 21, 2015 at 2:28 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Gromacs users, I am interested in simulation of lipid bilayers with Gromos96 53a6. As I understood this force field has been parametrized with reaction field instead of pme. Based on literatures, I have the following .mdp parameters: But I am not sure of those as my system has lots of LINCS warnings with these parameters. integrator = md tinit = 0 dt = 0.002 nsteps = 5 nstcomm = 1 comm-grps= nstxout = 0 nstvout = 0 nstfout = 0 nstenergy= 100 nstxtcout= 5000 xtc-precision = 1000 energygrps = system nstlist = 5 ns_type = grid pbc = xyz rlist = 0.8 coulombtype = reaction_field rcoulomb-switch= 0 rcoulomb = 1.4 epsilon_rf = 62 vdw-type = Cut-off rvdw-switch = 0 rvdw= 1.4 DispCorr = no tcoupl = v-rescale tc_grps = lipid water_ion tau_t =0.1 0.1 ref_t =353 353 Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.6e-5 4.6e-5 ref_p = 1.0 1.0 gen_vel= yes gen_temp = 353 gen_seed = 17352 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no shake-tol= 1e-04 morse= no Interestingly, when I use common Gromos parameters including pme, as follows, I do not have any LINCS problem with my system. integrator= md tinit= 0 dt = 0.002 nsteps = 5 pbc= xyz comm-mode = linear nstcomm= 1 comm-grps = system nstxout = 0 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid nstenergy = 100 nstxtcout = 5000 energygrps= system coulombtype = pme rcoulomb= 1.0 rlist= 1.0 vdw-type= cutoff rvdw = 1.0 DispCorr = no table-extension = 1 tcoupl = v-rescale tc-grps= lipid water_ion tau-t = 0.1 0.1 ref-t= 353 353 Pcoupl= berendsen Pcoupltype = semiisotropic ref-p= 1.0 1.0 tau-p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 constraints = all-bonds constraint-algorithm = Lincs gen_vel= yes gen_temp= 353 gen_seed= -1 Since the initial structures are the same, I think my parameters for reaction field one has problem. I have also tried shorter time steps (even 0.5 fs) and also started from different initial structures but the problem still exist. I searched the mailing list but I could not find my answer completely. Please let me know if you have any idea about parameters or if you
Re: [gmx-users] Gromos 53a6, .mdp parameters for reaction field
I looked at the first link, it was a useful discussion. Now, I am trying suggestions with rlist/r(columb/vdw)=(1.4/1.4) and everything is working properly till now. It seems the problem was the twin-range + RF with this version of Gromacs as has been discussed and you mentioned already. I am playing a little bit to see if I everything will be fine with the rest of test simulation. I will reply again after my tests. Thanks for the links Cheers Mohsen On Tue, Jul 21, 2015 at 4:21 PM, João M. Damas jmda...@itqb.unl.pt wrote: I really think you may be losing time with LINCS parameters. Look at these links too: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-March/088108.html http://redmine.gromacs.org/issues/1400 You use a twin-range, i.e. a rlist/r(coulomb/vdw) of 0.8/1.4, so I really think that this may be the source of your problems. The links that I sent you present solutions to your problem, but almost always at a computational cost, i.e. slower simulations. João On Tue, Jul 21, 2015 at 9:34 PM, V.V.Chaban vvcha...@gmail.com wrote: Maybe indeed downgrade to an earlier version. I, for sure, successfully used reaction field with gromacs 3-3-3 (imagine when it was). Professor Vitaly V. Chaban On Tue, Jul 21, 2015 at 4:49 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Hi Chaban, Me too, but I do not know why starting with the same initial structures and also starting from equilibrated structures again cause LINCS problems in one not in the other one. I have tried lincs-iter and lincs-order and also lincs allowable angle deviations but LINCS error still exist. This is why I think there is something wrong with other parameters, e.g. reaction field! Sure, I will look at epsilon_r, thanks. On Tue, Jul 21, 2015 at 11:44 AM, V.V.Chaban vvcha...@gmail.com wrote: I do not see much connection between bond constraints and treatment of electrostatics beyond the cut-off distance. There is also an epsilon_r keyword. I would investigate what exactly it means and whether it is used in the reaction field procedure. The all-bonds contraint often results in different problems. You will have to play with the relevant parameters, like lincs_order and allowable deviation. On Tue, Jul 21, 2015 at 2:28 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Gromacs users, I am interested in simulation of lipid bilayers with Gromos96 53a6. As I understood this force field has been parametrized with reaction field instead of pme. Based on literatures, I have the following .mdp parameters: But I am not sure of those as my system has lots of LINCS warnings with these parameters. integrator = md tinit = 0 dt = 0.002 nsteps = 5 nstcomm = 1 comm-grps= nstxout = 0 nstvout = 0 nstfout = 0 nstenergy= 100 nstxtcout= 5000 xtc-precision = 1000 energygrps = system nstlist = 5 ns_type = grid pbc = xyz rlist = 0.8 coulombtype = reaction_field rcoulomb-switch= 0 rcoulomb = 1.4 epsilon_rf = 62 vdw-type = Cut-off rvdw-switch = 0 rvdw= 1.4 DispCorr = no tcoupl = v-rescale tc_grps = lipid water_ion tau_t =0.1 0.1 ref_t =353 353 Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.6e-5 4.6e-5 ref_p = 1.0 1.0 gen_vel= yes gen_temp = 353 gen_seed = 17352 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no shake-tol= 1e-04 morse= no Interestingly, when I use common Gromos parameters including pme, as follows, I do not have any LINCS problem with my system. integrator= md tinit= 0 dt = 0.002 nsteps = 5 pbc= xyz comm-mode = linear nstcomm= 1 comm-grps = system nstxout = 0 nstvout = 0 nstfout = 0 nstlist
Re: [gmx-users] Gromos 53a6, .mdp parameters for reaction field
I really think you may be losing time with LINCS parameters. Look at these links too: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-March/088108.html http://redmine.gromacs.org/issues/1400 You use a twin-range, i.e. a rlist/r(coulomb/vdw) of 0.8/1.4, so I really think that this may be the source of your problems. The links that I sent you present solutions to your problem, but almost always at a computational cost, i.e. slower simulations. João On Tue, Jul 21, 2015 at 9:34 PM, V.V.Chaban vvcha...@gmail.com wrote: Maybe indeed downgrade to an earlier version. I, for sure, successfully used reaction field with gromacs 3-3-3 (imagine when it was). Professor Vitaly V. Chaban On Tue, Jul 21, 2015 at 4:49 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Hi Chaban, Me too, but I do not know why starting with the same initial structures and also starting from equilibrated structures again cause LINCS problems in one not in the other one. I have tried lincs-iter and lincs-order and also lincs allowable angle deviations but LINCS error still exist. This is why I think there is something wrong with other parameters, e.g. reaction field! Sure, I will look at epsilon_r, thanks. On Tue, Jul 21, 2015 at 11:44 AM, V.V.Chaban vvcha...@gmail.com wrote: I do not see much connection between bond constraints and treatment of electrostatics beyond the cut-off distance. There is also an epsilon_r keyword. I would investigate what exactly it means and whether it is used in the reaction field procedure. The all-bonds contraint often results in different problems. You will have to play with the relevant parameters, like lincs_order and allowable deviation. On Tue, Jul 21, 2015 at 2:28 PM, Mohsen Ramezanpour ramezanpour.moh...@gmail.com wrote: Dear Gromacs users, I am interested in simulation of lipid bilayers with Gromos96 53a6. As I understood this force field has been parametrized with reaction field instead of pme. Based on literatures, I have the following .mdp parameters: But I am not sure of those as my system has lots of LINCS warnings with these parameters. integrator = md tinit = 0 dt = 0.002 nsteps = 5 nstcomm = 1 comm-grps= nstxout = 0 nstvout = 0 nstfout = 0 nstenergy= 100 nstxtcout= 5000 xtc-precision = 1000 energygrps = system nstlist = 5 ns_type = grid pbc = xyz rlist = 0.8 coulombtype = reaction_field rcoulomb-switch= 0 rcoulomb = 1.4 epsilon_rf = 62 vdw-type = Cut-off rvdw-switch = 0 rvdw= 1.4 DispCorr = no tcoupl = v-rescale tc_grps = lipid water_ion tau_t =0.1 0.1 ref_t =353 353 Pcoupl = berendsen pcoupltype = semiisotropic tau_p = 1.0 1.0 compressibility = 4.6e-5 4.6e-5 ref_p = 1.0 1.0 gen_vel= yes gen_temp = 353 gen_seed = 17352 constraints = all-bonds constraint-algorithm = Lincs unconstrained-start = no shake-tol= 1e-04 morse= no Interestingly, when I use common Gromos parameters including pme, as follows, I do not have any LINCS problem with my system. integrator= md tinit= 0 dt = 0.002 nsteps = 5 pbc= xyz comm-mode = linear nstcomm= 1 comm-grps = system nstxout = 0 nstvout = 0 nstfout = 0 nstlist = 10 ns_type = grid nstenergy = 100 nstxtcout = 5000 energygrps= system coulombtype = pme rcoulomb= 1.0 rlist= 1.0 vdw-type= cutoff rvdw = 1.0 DispCorr = no table-extension = 1 tcoupl = v-rescale tc-grps= lipid water_ion tau-t = 0.1 0.1 ref-t= 353 353 Pcoupl= berendsen Pcoupltype
