at the box dimensions are small and thats the problem?
> Thanks,Mohammad
> From: Alex
> To: Discussion list for GROMACS users ;
> Discussion list for GROMACS users
> Sent: Friday, 14 July 2017, 11:31:06
> Subject: Re: [gmx-users] NPT problem
>
>
> >
> >
: [gmx-users] NPT problem
>
> I used "gmx x2top -f gr.gro -o topol1.top -ff cnt_oplsaa -name CNT
> -noparam -pbc" for generating the topology. then I used "gmx editconf
> -f grvmdn.pdb -o gr.gro -box 11 11 11 -angles 90 90 90" for creating
> the box
>
A
s ;
Mohammad Roostaie
*Sent:* Thursday, 13 July 2017, 22:51:48
*Subject:* Re: [gmx-users] NPT problem
Also, that tutorial's parameters that are completely wrong for
graphene. For bulk graphene bond types I suggest:
CJCJ 10.14200 420420.0
For bulk angles:
CJ CJ CJ
ards,Mohammad
From: Alex
To: Discussion list for GROMACS users ; Mohammad
Roostaie
Sent: Thursday, 13 July 2017, 22:51:48
Subject: Re: [gmx-users] NPT problem
Also, that tutorial's parameters that are completely wrong for graphene. For
bulk graphene bond types I suggest:
Also, that tutorial's parameters that are completely wrong for graphene.
For bulk graphene bond types I suggest:
CJCJ 10.14200 420420.0
For bulk angles:
CJ CJ CJ 1 120.000659.346
For bulk dihedrals:
CJ CJ CJ CJ 3 17.30770 0.0 -
It is very unclear what you mean by "the results were good" and then "the
results were not good." Your graphene setup is bad and it propagated to
everything else. Please do not start solvating your graphene sample prior
to making sure that your model is reasonable.
To diagnose what's wrong with you
Hi All GROMACS users,
I created graphene with nanotube modeler then I created a force field for
graphene based on OPLS (by using this link and its parameters:
http://chembytes.wikidot.com/grocnt). I generated the topology file using x2top
command. I put the graphene inside a box of water (TI
