[gmx-users] Graphene topology file
#SUKRITI GUPTA#
SUKRITI002 at e.ntu.edu.sg
Mon Jul 7 08:50:29 CEST 2014
Hi Abhijit,
Following is my mdp file:
; VARIOUS PREPROCESSING OPTIONS
title =
cpp = /lib/cpp
include =
define = -DFLEXIBLE
; RUN CONTROL PARAMETERS
integrator = l_bfgs
; Start time and timestep in ps
tinit = 0
dt = 0.001
nsteps = 5000
; For exact run continuation or redoing part of a run
init_step = 0
; mode for center of mass motion removal
comm-mode = Linear
; number of steps for center of mass motion removal
nstcomm = 1
; ENERGY MINIMIZATION OPTIONS
; Force tolerance and initial step-size
emtol = 10
emstep = 0.01
; Max number of iterations in relax_shells
niter = 20
; Step size (1/ps^2) for minimization of flexible constraints
fcstep = 0
; Frequency of steepest descents steps when doing CG
nstcgsteep = 1000
nbfgscorr = 10
; OUTPUT CONTROL OPTIONS
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout = 100
nstvout = 100
nstfout = 100
; Checkpointing helps you continue after 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
; This selects the subset of atoms for the xtc file. You can
; 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
rlist = 1.2
domain-decomposition = no
; OPTIONS FOR ELECTROSTATICS AND VDW
; Method for doing electrostatics
coulombtype = Cut-off
rcoulomb = 1.2
; Method for doing Van der Waals
vdw-type = Switch
; cut-off lengths
rvdw-switch = 0
rvdw = 1.0
; Apply long range dispersi0n corrections for Energy and Pressure
DispCorr = No
; Extension of the potential lookup tables beyond the cut-off
table-extension = 2
; Spacing for the PME/PPPM FFT grid
fourierspacing = 0.12
; FFT grid size, when a value is 0 fourierspacing will be used
fourier_nx = 0
fourier_ny = 0
fourier_nz = 0
; EWALD/PME/PPPM parameters
pme_order = 4
ewald_rtol = 4e-05
ewald_geometry = 3d
epsilon_surface = 0
optimize_fft = no
; GENERATE VELOCITIES FOR STARTUP RUN
gen-vel = no
gen-temp = 300
gen-seed = 173529
periodic_molecules=yes
freezegrps = GRA
freezedim = Y Y Y
________________________________
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 abhijit Kayal <abhijitchemiitd at gmail.com>
Sent: Monday, July 7, 2014 1:21 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Graphene topology file
Hi Sukriti,
Can you post your .mdp file of energy minimization? The problem is not
because there are no terminal H atoms. If you want periodic boundary
conditions only x-y direction
then you have to use nwall in .mdp file.
Thanks
Abhijit
On Mon, Jul 7, 2014 at 10:06 AM, #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg>
wrote:
> Hi all,
>
> After getting the topology file for graphene, when i tried to freeze
> graphene and do energy minimization with just water molecules around it,
> then the graphene structure becomes distorted ie. the upper layer of the
> graphene shifts down and the terminal carbons forms bond with each other. I
> think this happens because i did not add terminal hydrogens to the graphene
> sheet as I wanted periodic boundary conditions in x y direction. Also the
> box size in z direction is shown to be zero in the output file of energy
> minimization. Can anyone please let me know how to solve this problem?
>
> Thanks,
>
> Sukriti
>
> ________________________________
>
> 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 #SUKRITI
> GUPTA# <SUKRITI002 at e.ntu.edu.sg>
> Sent: Friday, July 4, 2014 5:10 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Graphene topology file
>
> Hi Abhijit,
>
> Thanks for the reply. Now it is working.
>
> Regards
> Sukriti
>
>
>
> ________________________________
>
> 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 abhijit
> Kayal <abhijitchemiitd at gmail.com>
> Sent: Friday, July 4, 2014 4:14 PM
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Graphene topology file
>
> Hi Sukirti,
>
> Try the following and additionally if you want force and angle constant you
> can also mention in g_x2top.
> g_x2top -f gra.pdb -o gra.top -name GRA -nexcl 3 -pbc
>
> You have to mention periodic_molecules=yes in the .mdp file.
>
> Thanks
> Abhijit
>
>
> On Fri, Jul 4, 2014 at 1:04 PM, #SUKRITI GUPTA# <SUKRITI002 at e.ntu.edu.sg>
> wrote:
>
> > Hi Abhijit,
> >
> > My g_x2top command is:
> > g_x2top -f gra_2.pdb -o graphene.top -ff oplsaa -name graphene -noparam
> > -pbc
> >
> > The grompp output is:
> >
> > ERROR 4100 [file graphene.top, line 10448]: ; (for all the lines, I
> > have copied here only one line.)
> > No default Ryckaert-Bell. types
> >
> > Excluding 3 bonded neighbours molecule type 'graphene'
> >
> > -------------------------------------------------------
> > Program grompp, VERSION 4.5.5
> > Source code file: /build/buildd/gromacs-4.5.5/src/kernel/toppush.c, line:
> > 1987
> >
> > Fatal error:
> > No such moleculetype SOL
> > For more information and tips for troubleshooting, please check the
> GROMACS
> > website at http://www.gromacs.org/Documentation/Errors
> >
> > Thanks
> > Sukriti
> >
> > ________________________________
> >
> > 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 abhijit
> > Kayal <abhijitchemiitd at gmail.com>
> > Sent: Friday, July 4, 2014 2:21 PM
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Graphene topology file
> >
> > Hi Sukriti,
> > Can you tell me the g_x2top command you have given and the grompp
> > output.
> >
> > Thanks
> > Abhijit
> >
> >
> > On Fri, Jul 4, 2014 at 10:01 AM, #SUKRITI GUPTA# <
> SUKRITI002 at e.ntu.edu.sg>
> > wrote:
> >
> > > Dear Justin and Abhijit,
> > >
> > > Thanks a lot for your help. Now I am able to make the topology file but
> > > while doing grompp for energy minimisation its not taking the dihedral
> > > values on its own.
> > >
> > > Regards
> > > Sukriti
> > > ________________________________
> > >
> > > 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
> abhijit
> > > Kayal <abhijitchemiitd at gmail.com>
> > > Sent: Thursday, July 3, 2014 6:43 PM
> > > To: gmx-users at gromacs.org; vvchaban at gmail.com
> > > Subject: Re: [gmx-users] Graphene topology file
> > >
> > > Hi Sukriti,
> > > Copy the oplsaa.ff directory to your working directory. Then in
> > > ffnonbonded.itp file add the following lines..
> > > opls_995 C 6 12.01100 0.000 A 3.40000e-01
> > > 3.61200e-01
> > > opls_996 C 6 12.01100 0.000 A 3.40000e-01
> > > 3.61200e-01
> > > opls_997 C 6 12.01100 0.000 A 3.40000e-01
> > > 3.61200e-01
> > >
> > > Then in atomname2type.n2t file add the following lines.
> > > C opls_995 0 12.011 2 C 0.142 C 0.142
> > > C opls_996 0 12.011 3 C 0.142 C 0.142 C 0.142
> > > C opls_997 0 12.011 1 C 0.142
> > >
> > > Then use g_x2top. This will work.
> > >
> > > Thanks
> > > Abhijit
> > >
> > >
> > > On Thu, Jul 3, 2014 at 3:11 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>
> > > wrote:
> > >
> > > > Graphene topology is like for tube, so
> > > >
> > > > C .... C
> > > > C ... C ... C
> > > > C .... C ....C .... C
> > > >
> > > > to the N2T file and you are done.
> > > >
> > > >
> > > > Dr. Vitaly V. Chaban
> > > >
> > > >
> > > > On Wed, Jul 2, 2014 at 5:29 PM, Justin Lemkul <jalemkul at vt.edu>
> wrote:
> > > > >
> > > > >
> > > > > On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote:
> > > > >>
> > > > >> Dear all,
> > > > >>
> > > > >>
> > > > >> I want to simulate graphite in water, for which i am trying to
> > create
> > > a
> > > > >> topology file for graphite. As its .rtp file cannot be written
> > > > correctly, i
> > > > >> tried to use g_x2top command following the steps given in
> following
> > > > >> tutorial.
> > > > >>
> > > > >> http://chembytes.wikidot.com/grocnt
> > > > >>
> > > > >>
> > > > >> But I think this tutorial is quite old and hence suitable for
> older
> > > > >> version of gromacs as it still uses FF.dat file. Moreover if i am
> > > > trying to
> > > > >> make a new forcefield directory with name graphite_oplsaa
> containing
> > > the
> > > > >> modified files like .n2t,.rtp and .itp, its giving me an error
> that
> > > > "Could
> > > > >> not find force field 'graphite_oplsaa' in current directory,
> install
> > > > tree or
> > > > >> GMXDATA path". When I try to add this forcefield in original path
> > ie.
> > > > >> user/share/gromacs/top, it does not allow me to do that as i am
> not
> > > the
> > > > >> administrator. Can anyone please let me know how to create the
> > > topology
> > > > >> file. I require 3 graphene sheets with pbc. I have created the
> .pdb
> > > file
> > > > >> using nanobuilder in vmd.
> > > > >>
> > > > >
> > > > > The tutorial is indeed outdated but the logic is fairly sound. You
> > > don't
> > > > > have to modify anything in $GMXLIB (system-wide); you can just
> create
> > > an
> > > > > .n2t file in the working directory and it will override the one at
> > the
> > > > force
> > > > > field level.
> > > > >
> > > > > -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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> > >
> > > --
> > > Abhijit kayal
> > > Research Scholar
> > > Theoretical Chemistry
> > > IIT Kanpur
> > > --
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> >
> >
> > --
> > Abhijit kayal
> > Research Scholar
> > Theoretical Chemistry
> > IIT Kanpur
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>
> --
> Abhijit kayal
> Research Scholar
> Theoretical Chemistry
> IIT Kanpur
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Abhijit kayal
Research Scholar
Theoretical Chemistry
IIT Kanpur
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