[gmx-users] Graphene topology file

[Justin Lemkul]

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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