On 4/21/14, 5:48 PM, mirc...@sjtu.edu.cn wrote:
Hi everyone, I am using GROMACS to simulate bilayers, and I am testing two sets of parameters at present. However, I found significant differences of simulation speed of these two parameters sets. The mainly differences between these parameters are the cut off parameters or of the VDW and coulomb interactions, in the first parameter set, a cut off of 1.0 nm was used for both of the VDW and the coulomb interactions. In the second parameter set, a cut off 1.4 was used for the coulomb interactions, whereas a switch from 1.4 nm to 1.5 nm was used for the VDW parameters. Under the first parameter set, my system could run about 20 ns per day, whereas for the second parameter set, my system only run 7-8 ns per day. So I am wondering if this is only raised because of the cut off parameters? And is this a normal pheonomen?
Yes, it's normal. The most important thing to know is you need to use the parameters for which the force field was designed. Lipids are extremely sensitive to changes in the cutoff. Varying these values is very hazardous, so if you're doing something non-standard, you'd better have a lot of good proof that what you're doing isn't going to lead to artifacts.
-Justin
I am listing the mdp file at the end of this email. Please note the only relevarent differences between these two parameter sets are the cut off differences. With my best regards, rxgu -------------------------------------------- the first parameter set: title = NPT Equilibration integrator = md nsteps = 25000000 dt = 0.002 nstxout = 0 nstvout = 0 nstenergy = 1000 nstlog = 2000 nstxtcout = 2000 xtc-precision = 10000 constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ;cutoff-scheme = Verlet ns_type = grid nstlist = 10 rlist = 1.0 coulombtype = PME rcoulomb = 1.0 vdwtype = cut-off rvdw = 1.0 DispCorr = EnerPres pme_order = 4 fourierspacing = 0.12 optimize_fft = yes pbc = xyz tcoupl = V-rescale tc-grps = POPC SOL tau_t = 0.5 0.5 ref_t = 323 323 pcoupl = Berendsen pcoupltype = semiisotropic tau_p = 10.0 10.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 gen_vel = yes gen_temp = 323 gen_seed = 82907543 comm-mode = Linear comm-grps = system ---------------------------------------------------------------- the second parameter set: title = NPT Equilibration integrator = md nsteps = 25000000 dt = 0.002 nstxout = 0 nstvout = 0 nstenergy = 1000 nstlog = 2000 nstxtcout = 2000 xtc-precision = 10000 constraint_algorithm = lincs constraints = all-bonds lincs_iter = 1 lincs_order = 4 ;cutoff-scheme = Verlet ns_type = grid nstlist = 10 rlist = 1.4 rlistlong = 1.7 coulombtype = PME rcoulomb = 1.4 vdwtype = Switch rvdw = 1.5 rvdw-switch = 1.4 DispCorr = EnerPres pme_order = 4 fourierspacing = 0.12 optimize_fft = yes pbc = xyz tcoupl = V-rescale tc-grps = POPC SOL tau_t = 0.5 0.5 ref_t = 323 323 pcoupl = Berendsen pcoupltype = semiisotropic tau_p = 10.0 10.0 ref_p = 1.0 1.0 compressibility = 4.5e-5 4.5e-5 gen_vel = yes gen_temp = 323 gen_seed = 82907543 comm-mode = Linear comm-grps = System --------------------------------------------------------------------------------------
-- ================================================== 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.
