Re: [gmx-users] Dynamics only for cavity in molecule.
Hi, I have no idea whether that will help. Even if it is better, I am struggling to see that annealing and freeze groups is a useful model, even with frozen solvent. Mark On Fri, 4 Aug 2017 21:40 wrote: > Well, that means that I need to use the group scheme? > Or I can just add solvent and run the same thing? > > > Hi, > > > > I imagine nobody has ever tried with Verlet plus freeze plus annealing, > so > > it could be broken somehow... But frozen atoms around a cavity and no > > electric field from solvent sounds like a model highly unlikely to be > > related to reality... > > > > Mark > > > > On Fri, 4 Aug 2017 18:55 wrote: > > > >> Hello! > >> > >> I want to run dynamics only for a relatively small cavity of my > >> molecule, > >> with all other atoms frozen. For this reason, I also don't use solvent, > >> because it won't move anyway. I run the simulation on GPU (gromacs > >> 5.1.2), > >> i.e. I use the Verlet scheme, pbc = xyz. However, when I start running > >> simulations, I get violent behavior: the molecule immediately falls > >> apart!! I am sure that I just made a silly thing in the parameters, but > >> what is it? Here I attach my dynamics .mdp parameters: > >> > >> > >> define = -DPOSRES > >> integrator = md > >> dt = 0.001 > >> nsteps = 120 > >> > >> nstxout = 1000 > >> nstvout = 1000 > >> nstxtcout = 1000 > >> nstlog = 100 > >> nstenergy = 1000 > >> > >> continuation = no > >> constraints= none > >> > >> tcoupl = V-rescale > >> tc_grps = System > >> tau_t = 0.1 > >> ref_t = 0 > >> > >> cutoff-scheme = Verlet > >> ns_type = grid > >> nstlist = 10 > >> rcoulomb = 0.9 > >> rvdw = 0.9 > >> > >> coulombtype = PME > >> pme_order = 4 > >> fourierspacing = 0.16 > >> > >> pbc = xyz > >> gen_vel = no > >> > >> DispCorr = EnerPres > >> > >> ; > >> ; Freezing atoms # this is all the atoms except for the cavity inside > >> ; > >> freezegrps = GroupDyna > >> freezedim = Y Y Y > >> ; > >> ; Heating > >> ; > >> annealing = single > >> annealing_npoints = 2 > >> annealing_time = 0 50 > >> annealing_temp = 0 298 > >> > >> > >> Thank you in advance, > >> Dmitrii. > >> > >> > >> -- > >> 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. > > > > > -- > 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] Dynamics only for cavity in molecule.
Well, that means that I need to use the group scheme? Or I can just add solvent and run the same thing? > Hi, > > I imagine nobody has ever tried with Verlet plus freeze plus annealing, so > it could be broken somehow... But frozen atoms around a cavity and no > electric field from solvent sounds like a model highly unlikely to be > related to reality... > > Mark > > On Fri, 4 Aug 2017 18:55 wrote: > >> Hello! >> >> I want to run dynamics only for a relatively small cavity of my >> molecule, >> with all other atoms frozen. For this reason, I also don't use solvent, >> because it won't move anyway. I run the simulation on GPU (gromacs >> 5.1.2), >> i.e. I use the Verlet scheme, pbc = xyz. However, when I start running >> simulations, I get violent behavior: the molecule immediately falls >> apart!! I am sure that I just made a silly thing in the parameters, but >> what is it? Here I attach my dynamics .mdp parameters: >> >> >> define = -DPOSRES >> integrator = md >> dt = 0.001 >> nsteps = 120 >> >> nstxout = 1000 >> nstvout = 1000 >> nstxtcout = 1000 >> nstlog = 100 >> nstenergy = 1000 >> >> continuation = no >> constraints= none >> >> tcoupl = V-rescale >> tc_grps = System >> tau_t = 0.1 >> ref_t = 0 >> >> cutoff-scheme = Verlet >> ns_type = grid >> nstlist = 10 >> rcoulomb = 0.9 >> rvdw = 0.9 >> >> coulombtype = PME >> pme_order = 4 >> fourierspacing = 0.16 >> >> pbc = xyz >> gen_vel = no >> >> DispCorr = EnerPres >> >> ; >> ; Freezing atoms # this is all the atoms except for the cavity inside >> ; >> freezegrps = GroupDyna >> freezedim = Y Y Y >> ; >> ; Heating >> ; >> annealing = single >> annealing_npoints = 2 >> annealing_time = 0 50 >> annealing_temp = 0 298 >> >> >> Thank you in advance, >> Dmitrii. >> >> >> -- >> 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. > -- 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] Dynamics only for cavity in molecule.
Hi, I imagine nobody has ever tried with Verlet plus freeze plus annealing, so it could be broken somehow... But frozen atoms around a cavity and no electric field from solvent sounds like a model highly unlikely to be related to reality... Mark On Fri, 4 Aug 2017 18:55 wrote: > Hello! > > I want to run dynamics only for a relatively small cavity of my molecule, > with all other atoms frozen. For this reason, I also don't use solvent, > because it won't move anyway. I run the simulation on GPU (gromacs 5.1.2), > i.e. I use the Verlet scheme, pbc = xyz. However, when I start running > simulations, I get violent behavior: the molecule immediately falls > apart!! I am sure that I just made a silly thing in the parameters, but > what is it? Here I attach my dynamics .mdp parameters: > > > define = -DPOSRES > integrator = md > dt = 0.001 > nsteps = 120 > > nstxout = 1000 > nstvout = 1000 > nstxtcout = 1000 > nstlog = 100 > nstenergy = 1000 > > continuation = no > constraints= none > > tcoupl = V-rescale > tc_grps = System > tau_t = 0.1 > ref_t = 0 > > cutoff-scheme = Verlet > ns_type = grid > nstlist = 10 > rcoulomb = 0.9 > rvdw = 0.9 > > coulombtype = PME > pme_order = 4 > fourierspacing = 0.16 > > pbc = xyz > gen_vel = no > > DispCorr = EnerPres > > ; > ; Freezing atoms # this is all the atoms except for the cavity inside > ; > freezegrps = GroupDyna > freezedim = Y Y Y > ; > ; Heating > ; > annealing = single > annealing_npoints = 2 > annealing_time = 0 50 > annealing_temp = 0 298 > > > Thank you in advance, > Dmitrii. > > > -- > 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.
[gmx-users] Dynamics only for cavity in molecule.
Hello! I want to run dynamics only for a relatively small cavity of my molecule, with all other atoms frozen. For this reason, I also don't use solvent, because it won't move anyway. I run the simulation on GPU (gromacs 5.1.2), i.e. I use the Verlet scheme, pbc = xyz. However, when I start running simulations, I get violent behavior: the molecule immediately falls apart!! I am sure that I just made a silly thing in the parameters, but what is it? Here I attach my dynamics .mdp parameters: define = -DPOSRES integrator = md dt = 0.001 nsteps = 120 nstxout = 1000 nstvout = 1000 nstxtcout = 1000 nstlog = 100 nstenergy = 1000 continuation = no constraints= none tcoupl = V-rescale tc_grps = System tau_t = 0.1 ref_t = 0 cutoff-scheme = Verlet ns_type = grid nstlist = 10 rcoulomb = 0.9 rvdw = 0.9 coulombtype = PME pme_order = 4 fourierspacing = 0.16 pbc = xyz gen_vel = no DispCorr = EnerPres ; ; Freezing atoms # this is all the atoms except for the cavity inside ; freezegrps = GroupDyna freezedim = Y Y Y ; ; Heating ; annealing = single annealing_npoints = 2 annealing_time = 0 50 annealing_temp = 0 298 Thank you in advance, Dmitrii. -- 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.
[gmx-users] Dynamics only for cavity in molecule.
Hello! I want to run dynamics only for a relatively small cavity of my molecule, with all other atoms frozen. For this reason, I also don't use solvent, because it won't move anyway. I run the simulation on GPU (gromacs 5.1.2), i.e. I use the Verlet scheme, pbc = xyz. However, when I start running simulations, I get violent behavior: the molecule immediately falls apart!! I am sure that I just made a silly thing in the parameters, but what is it? Here I attach my dynamics .mdp parameters: define = -DPOSRES integrator = md dt = 0.001 nsteps = 120 nstxout = 1000 nstvout = 1000 nstxtcout = 1000 nstlog = 100 nstenergy = 1000 continuation = no constraints= none tcoupl = V-rescale tc_grps = System tau_t = 0.1 ref_t = 0 cutoff-scheme = Verlet ns_type = grid nstlist = 10 rcoulomb = 0.9 rvdw = 0.9 coulombtype = PME pme_order = 4 fourierspacing = 0.16 pbc = xyz gen_vel = no DispCorr = EnerPres ; ; Freezing atoms # this is all the atoms except for the cavity inside ; freezegrps = GroupDyna freezedim = Y Y Y ; ; Heating ; annealing = single annealing_npoints = 2 annealing_time = 0 50 annealing_temp = 0 298 Thank you in advance, Dmitrii. -- 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.
