(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? 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 | (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
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