On 3/15/17 3:09 PM, Davit Hakobyan wrote:
Dear All, I try to run a simulation with protein-membrane system in charmm36 ff with Gromacs5.0.4 and the simulation runs without complain.The problem is in the unit cell size which seems to grow during a short 500 ps simulation from ~15 to ~28 nm in Z direction although the system atoms remain confined in the~15 nm in Z direction. The GRO files before and after the 500 ps simulation can be downloaded from the following link: https://uni-muenster.sciebo.de/index.php/s/GBHjED2t1KzZZ2o
Your initial coordinates are badly fragmented, with regions of vacuum and isolated water molecules. You're going to get bizarre behavior as the system collapses to try to close those voids. This outcome likely isn't a function of .mdp settings, but unphysical initial coordinates.
<snip> Bonus comments!
MDP Parameters (OLD) ------------------------------------------------- integrator = md dt = 0.002 nsteps = 250000000 nstxout = 500000 nstvout = 500000 nstlog = 100000 nstenergy = 500000 nstxtcout = 500000 xtc_grps = energygrps = Protein CHL1 POPC DOPC POPS Water_and_ions ;energygrp_table = nstcalcenergy = 500 nstlist = 10 nstcomm = 50 comm_mode = Linear comm-grps = ns_type = grid rlist = 1.0 rlistlong = 1.4 rvdw_switch = 0.8 vdwtype = Switch
This is a potential switch, not a force switch, so lipid simulations done with these settings will have artificial behavior. Force switching is standard for all CHARMM additive force field simulations, and is absolutely required for lipids.
coulombtype = pme rcoulomb = 1.0 rcoulomb_switch = 0.0 rvdw = 1.2 fourierspacing = 0.15 pme_order = 6 ;ewald_rtol = 1e-6 tcoupl = V-rescale ;nose-hoover nhchainlength = 1 tc-grps = Protein CHL1 POPC DOPC POPS Water_and_ions
Coupling all different types of molecules in the system to their own thermostats is inappropriate.
-Justin
tau_t = 0.1 0.1 0.1 0.1 0.1 0.1 ref_t = 293 293 293 293 293 293 Pcoupl = parrinello-rahman ;berendsen ;parrinello-rahman Pcoupltype = semiisotropic tau_p = 5.0 compressibility = 4.5e-5 4.5e-5 ref_p = 1.0 1.0 pbc = xyz gen_vel = no ;yes gen_temp = 293 optimize_fft = yes constraints = hbonds continuation = no constraint_algorithm = Lincs lincs-order = 4 ; 8 is needed for BD with large time-steps. lincs-iter = 1 ; 1 is fine for normal simulations, but use 2 to conserve energy in NVE runs. ------------------------------------------------- In the new parameters I also tried to change the tcoupl from Nose-Hoover to V-rescale, but the outcome is the same, the box size becomes large. ProbablyI am missing something trivial. Does anybody have a clue what might be wrong? Thanks very much for any help. Davit
-- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 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.
