Hi Justin, Thanks for the reply. Following is my npt.mdp file for pbc in xy direction:
title = example cpp = define = -DFLEXIBLE 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 ; 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 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? Regards Sukriti Gupta ________________________________ Sukriti Gupta (Ms) | PhD Student | Energy Research Institute @ NTU (ERI@N) | Nanyang Technological University Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459) Tel: (65) 81164191 GMT+8h | Email:sukriti...@e.ntu.edu.sg | Web:erian.ntu.edu.sg ________________________________________ From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Justin Lemkul <jalem...@vt.edu> Sent: Thursday, July 10, 2014 8:28 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Graphene topology file On 7/10/14, 1:29 AM, #SUKRITI GUPTA# wrote: > Hi Justin, > > I did simulation 2 times, once with PBC in xy with walls and other time with > pbc in xyz. > > For pbc in xy with walls with following wall parameters: > > nwall = 2 > wall_type = 12-6 > wall_density = 5 5 > wall_atomtype = opls_995 opls_996 > wall_r_linpot = 1 > wall_ewald_zfac = 3 > > Energy minimization runs fine but npt shows following errror and is > terminated: > > Step 20: > The charge group starting at atom 796 moved than the distance allowed by the > domain decomposition in direction X > distance out of cell -0.290927 > New coordinates: 2.411 2.006 0.982 > Old cell boundaries in direction X: 0.000 2.702 > New cell boundaries in direction X: 0.000 2.702 > ------------------------------------------------------- > Program mdrun, VERSION 4.5.5 > Source code file: /build/buildd/gromacs-4.5.5/src/mdlib/domdec.c, line: 4124 > > Fatal error: > A charge group moved too far between two domain decomposition steps > This usually means that your system is not well equilibrated > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > For pbc in xyz, both energy minimization and npt run but the water is > suddenly moving far away from the graphene sheet any tries to agglomerate > together causing the box size to increase drastically. It is almost like the > box is about to explode. Its size changes from (2.70200 2.55300 4.00000) > to (11.46117 10.82915 16.96695). The box expands in x,y and z all > directions. > Without full .mdp files and some images demonstrating what's going on, it's too hard to guess at what's happening here. -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. -- 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.
