On 7/10/14, 8:46 AM, #SUKRITI GUPTA# wrote:
Hi Justin, Thanks for the reply. Following is my npt.mdp file for pbc in xy direction: title = example cpp = define = -DFLEXIBLE
You shouldn't use flexible water during MD. The water models in Gromacs were designed to be rigid.
constraints = none integrator = md dt = 0.001 nsteps = 100000 ;Output control parameters nstxout = 100 nstvout = 100 nstfout = 0 ;Checking for crashes nstcheckpoint = 1000 ; Output frequency for energies to log file and energy file nstlog = 100 nstenergy = 100 ; Output frequency and precision for xtc file nstxtcout = 0 xtc-precision = 1000 ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns-type = Grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xy ; nblist cut-off domain-decomposition= no rlist = 1.2 ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = Cut-off rcoulomb-switch = 0 rcoulomb = 1.2 ; ; Method for doing Van der Waals vdw-type = Switch ; cut-off lengths rvdw-switch = 0 rvdw = 1.0 ; OPTIONS FOR WEAK COUPLING ALGORITHMS ; Temperature coupling = yes tcoupl = Berendsen
The Berendsen algorithm has known deficiencies. For initial equilibration, it's OK, but don't use it for a production simulation.
; Groups to couple separately tc-grps = Other SOL ; Time constant (ps) and reference temperature (K) tau-t = .25 .25 ref-t = 300 300 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) tau-p = 1 1 compressibility = 0 4.5e-5 ref-p = 1.01325 1.01325 ; ; GENERATE VELOCITIES FOR STARTUP RUN gen-vel = yes gen-temp = 300 gen-seed = 173529 nwall = 2 wall_type = 12-6 wall_density = 5 5 wall_atomtype = opls_995 opls_996 wall_r_linpot = 1 wall_ewald_zfac = 3 periodic_molecules=yes freezegrps = GRA freezedim = Y Y Y
Freezing the graphene is probably going to generate a lot of problems. You get totally unphysical forces unless you use energygrp_excl properly, but even then, freezing is a severe perturbation to the system.
For pbc in xyz, nwall options are not there and I used Isotropic Pcoupletype with compressibility 4.5e-5. Gromacs Userlist is not allowing me to attach images as the size of the mail is increasing to more than 50KB. So can I mail the images to your mail id?
No. Post them to an image-sharing site and provide a URL. -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.
