[gmx-users] negative values of force
Justin A. Lemkul
jalemkul at vt.edu
Sat Aug 14 19:50:05 CEST 2010
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
> *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
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> -- gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users