Lod,
I asked a similar question some time ago but it apparently was lost in the
Internet.
What I have found, and what I think may help you, is contained in this
thread:
http://archive.ambermd.org/201804/0051.html
Read all the posts in the thread and I believe your question " Extract Force
from MDCRD/DCD trj" will be resolved.
Jim
-----Original Message-----
From: Lod King <lodking407.gmail.com>
Sent: Friday, July 27, 2018 2:40 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Extract Force from MDCRD/DCD trj
Hi Hai
I used the following commands:
>parm xxx.prmtop
>trajin md01.mdcrd
>trajout md01_1.out
>go
however, I obtained a very big output file (like 20GB, my mdcrd is also
20GB), with numbers which seems randomized, I dont see any "force to atom"
patten specifically.
On Wed, Jul 25, 2018 at 8:33 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> You can use either cpptraj or pytraj (Python interface of cpptraj) for
> that
>
> In [5]: import pytraj as pt
>
>
> In [6]: traj = pt.iterload('systemVF.nc', top='systemVF.parm7')
>
>
> In [7]: for f in traj: print(f.force)
>
> Hai
>
> On Wed, Jul 25, 2018 at 8:50 PM, Lod King <lodking407.gmail.com> wrote:
>
> > Hi all,
> >
> > I included ntwf = -f in my input parameters to run MD, and obtain a
> > 10ns
> of
> > mdcrd, how can I can extract force from this mdcrd file ? or Does
> > VMD can do any usual analysis from that?
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 27 2018 - 15:30:02 PDT
