On Oct 6, 2014 3:57 PM, "Atila Petrosian" wrote:
>
> Dear Mark
>
> Very thanks for you reply.
>
> I solved previous problem by swapping the order of my #include statements
> in forcefield.itp file.
>
> I used grompp for energy minimization, I obtained em.tpr file without any
> problem. Then I used
my em.mdp file is as follows:
integrator = steep
nsteps = 5
nstcomm = 1
emtol= 10
emstep = 0.01
ns_type = grid
rlist= 0.8
coulombtype = cut-off
vdwtype
Dear Mark
Very thanks for you reply.
I solved previous problem by swapping the order of my #include statements
in forcefield.itp file.
I used grompp for energy minimization, I obtained em.tpr file without any
problem. Then I used mdrun for energy minimization, this step was done
without error, b
You probably need to define [atomtypes] before you can define [bondtypes]
that use them. So swap the order of your #include statements.
Mark
On Mon, Oct 6, 2014 at 6:18 AM, Atila Petrosian
wrote:
> Dear gromacs users
>
> I want to do MD simulation of a CNT.
>
> I used aromatic carbon from charm
Dear gromacs users
I want to do MD simulation of a CNT.
I used aromatic carbon from charmm.ff
I created a cnt.ff folder containing following files:
ffcnt.atp:
---
CA12.01100 ;aromatic C
-
ffcnt.n2t:
You're including that file from somewhere that violates the rules in
chapter 5. But only you know where.
Mark
On Nov 26, 2013 11:07 AM, "Elham Gholamrezai"
wrote:
> Dear all
>
> I am working on simulation of hydrogen adsorption on
> graphene sheet, and I need to adopte my force field parameters
Dear all
I am working on simulation of hydrogen adsorption on
graphene sheet, and I need to adopte my force field parameters, new
force field folder is made and put in top directory of gromacs. For this
reason, I modified "charmm27.ff" and included new files (bond.itp,
nonbond.itp, n2t, atp,
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On 26 Nov 2013, at 08:39, Elham Gholamrezai wrote:
>
>
>
>
>
>
>
> Dear all
>
> I am working on simulation of hydrogen adsorption on graphene sheet, and I
> need to adopte my force field
Dear all
I am working on simulation of hydrogen adsorption on graphene sheet, and I need
to adopte my force field parameters, new force field folder is made and put in
top directory of gromacs. For this reason, I modified "charmm27.ff" and
included new files (bond.itp, nonbond.itp, n2t,
