[gmx-users] negative values of force
psamrat10 at yahoo.com
Sat Aug 14 19:47:46 CEST 2010
(1) I have got the pull.xvg file from the simulation. But there the data
resolution is very high e.g after every 2 ps. But I don' need that. So, I tried
to create a new .xvg file with lower resolution of data e.g. after every 50 ps.
So, I used the g_traj command.
(2) So, there is no error in getting the negative value of force, right?
(3) I have also created a dist.xvg file by applying g_dist command. Can I use
force.xvg (created by g_traj) and dist.xvg (created by g_dist) files to get
force vs. extension profile?
From: Justin A. Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Sat, August 14, 2010 10:34:25 AM
Subject: Re: [gmx-users] negative values of force
Samrat Pal wrote:
> Dear All,
> I have pulled a protein by keeping n-terminus fixed and pulling
>the c-terminus. I tried to extract the force.xvg profile from the .trr file by
>the following command -
If you've applied the pull code, is there some reason that the pullf.xvg file
does not contain the information you're looking for?
> g_traj -f traj.trr -s pull.tpr -of force.xvg
> But in the force.xvg profile I am getting both positive and negative values of
>force. What does it mean? Please suggest.
Simple Newtonian physics. g_traj is extracting instantaneous forces on the
constituent atoms, as stored in the .trr file, so all effects are considered -
pull force, intermolecular collisions, etc.
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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