Samrat Pal wrote:
(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.
Then you should have chosen a better value of pull_nstfout. Otherwise, you can
write a simple script to parse out data at more useful intervals.
(2) So, there is no error in getting the negative value of force, right?
No. Force is a vector quantity. Depending on the direction of motion of a
particular atom, the force may be moving it in a positive or negative direction.
This is very fundamental physics.
(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?
Again, the actual pull output (pullx.xvg) should be a suitable match for your
pullf.xvg data.
-Justin
Best
Samrat
------------------------------------------------------------------------
*From:* Justin A. Lemkul <[email protected]>
*To:* Discussion list for GROMACS users <[email protected]>
*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
> Samrat
-- ========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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