[gmx-users] Graphene topology file

Thu Jul 10 14:46:41 CEST 2014

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 at N) | Nanyang Technological University
Interdisciplinary Graduate School | Office: N1.3-B4-14, 62 Nanyang Drive, Singapore(637459)
Tel: (65) 81164191 GMT+8h | Email:sukriti002 at e.ntu.edu.sg | Web:erian.ntu.edu.sg

________________________________________
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 8:28 PM
To: gmx-users at 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

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

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