Re: [gmx-users] rlist for implicit water
On 6/3/14, 4:15 AM, Urszula Uciechowska wrote: Dear Gromacs users, I would like to run simulations with implicit water. My protein system is quite big it contains 784AA. I prepared eM.mdp file (see below) however I am not sure if its ok especially the rlist what should I use there in case of such big system. define = -DFLEXIBLE constraints = none integrator = steep ; steepest descents energy minimization dt = 0.001 ; ps nsteps = 3000 ; maximum number of steps to integrate implicit_solvent= GBSA gb_algorithm= Still nstgbradii = 1 gb_epsilon_solvent = 80 gb_saltconc = 0 sa_algorithm= Ace-approximation sa_surface_tension = -1 pbc = no rgbradii= 0 ns_type = simple; method of updating neighbor list nstlist = 0 rlist = 0 ; this means all-vs-all (no cut-off) coulombtype = cut-off rcoulomb= 0 ; [nm] distance for Coulomb cut-off vdwtype = cut-off ; twin-range cut-off with rlist where rvdw = rlist rvdw= 0 ; [nm] distance for LJ cut-off nstenergy = 100 emtol = 5.0 emstep = 0.01 comm-grps = Protein optimize_fft= yes Thank you in advance for any comments and suggestions. If you're using infinite cutoffs, the only acceptable value for rlist is 0. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- 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] rlist for implicit water
Dear Justin, How could I change the cut-offs to make the MD more faster in my case? /Urszula On 6/3/14, 4:15 AM, Urszula Uciechowska wrote: Dear Gromacs users, I would like to run simulations with implicit water. My protein system is quite big it contains 784AA. I prepared eM.mdp file (see below) however I am not sure if its ok especially the rlist what should I use there in case of such big system. define = -DFLEXIBLE constraints = none integrator = steep ; steepest descents energy minimization dt = 0.001 ; ps nsteps = 3000 ; maximum number of steps to integrate implicit_solvent= GBSA gb_algorithm= Still nstgbradii = 1 gb_epsilon_solvent = 80 gb_saltconc = 0 sa_algorithm= Ace-approximation sa_surface_tension = -1 pbc = no rgbradii= 0 ns_type = simple; method of updating neighbor list nstlist = 0 rlist = 0 ; this means all-vs-all (no cut-off) coulombtype = cut-off rcoulomb= 0 ; [nm] distance for Coulomb cut-off vdwtype = cut-off ; twin-range cut-off with rlist where rvdw = rlist rvdw= 0 ; [nm] distance for LJ cut-off nstenergy = 100 emtol = 5.0 emstep = 0.01 comm-grps = Protein optimize_fft= yes Thank you in advance for any comments and suggestions. If you're using infinite cutoffs, the only acceptable value for rlist is 0. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- 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. - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- 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] rlist for implicit water
On 6/3/14, 12:21 PM, Urszula Uciechowska wrote: Dear Justin, How could I change the cut-offs to make the MD more faster in my case? Well, there are plenty of things one can do to improve performance, but the better question is whether or not one can maintain something physically sensible at the same time :) For implicit solvent, at least in my own experience, the only way I get stable trajectories is with the infinite cutoff approach. Some advocate a long cutoff scheme with all cutoffs set to something like 2.0 or 4.0 nm, but that's never worked for me, either. You also should never judge performance from EM alone. -Justin /Urszula On 6/3/14, 4:15 AM, Urszula Uciechowska wrote: Dear Gromacs users, I would like to run simulations with implicit water. My protein system is quite big it contains 784AA. I prepared eM.mdp file (see below) however I am not sure if its ok especially the rlist what should I use there in case of such big system. define = -DFLEXIBLE constraints = none integrator = steep ; steepest descents energy minimization dt = 0.001 ; ps nsteps = 3000 ; maximum number of steps to integrate implicit_solvent= GBSA gb_algorithm= Still nstgbradii = 1 gb_epsilon_solvent = 80 gb_saltconc = 0 sa_algorithm= Ace-approximation sa_surface_tension = -1 pbc = no rgbradii= 0 ns_type = simple; method of updating neighbor list nstlist = 0 rlist = 0 ; this means all-vs-all (no cut-off) coulombtype = cut-off rcoulomb= 0 ; [nm] distance for Coulomb cut-off vdwtype = cut-off ; twin-range cut-off with rlist where rvdw = rlist rvdw= 0 ; [nm] distance for LJ cut-off nstenergy = 100 emtol = 5.0 emstep = 0.01 comm-grps = Protein optimize_fft= yes Thank you in advance for any comments and suggestions. If you're using infinite cutoffs, the only acceptable value for rlist is 0. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- 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. - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA 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 http://mackerell.umaryland.edu/~jalemkul == -- 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.
