Thanks a lot. Best Samrat
________________________________ From: Justin A. Lemkul <[email protected]> To: Gromacs Users' List <[email protected]> Sent: Sat, August 14, 2010 10:50:05 AM Subject: Re: [gmx-users] negative values of force 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 > > ======================================== > -- gmx-users mailing list [email protected] ><mailto:[email protected]> > http://lists.gromacs.org/mailman/listinfo/gmx-users > 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 [email protected] ><mailto:[email protected]>. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ======================================== 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 ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
