[gmx-users] Graphene topology file

[#SUKRITI GUPTA#]

Hi Justin,

Thanks for the reply. I changed  define= -dflexible to -dposres_water and removed freeze graphene group in my .mdp file and ran the energy minimization and npt again. This time for pbc= xyz, the water doesn't fly away but the graphene sheet curves and does not remain in xy plane. Is it ok for the sheet to bend during simulation and will it not effect the pbc?

Also for pbc=xy, the same problem persists as the previous one i.e. following error occurs:

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.

Can you please suggest what can be causing the error to occur?

Thanks and Regards
Sukriti


________________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Thursday, July 10, 2014 8:50 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Graphene topology file

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================
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