[gmx-users] negative values of force

Samrat Pal 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.


> Samrat 

-- ========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080

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