<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:times new roman,new york,times,serif;font-size:12pt"><div>(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.<br><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">(2) So, there is no error in getting the negative value of force, right? <br><br>(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?<br>Best<br>Samrat<br><div style="font-family: arial,helvetica,sans-serif; font-size: 13px;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight:
bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Sat, August 14, 2010 10:34:25 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] negative values of force<br></font><br>
<br><br>Samrat Pal wrote:<br>> Dear All,<br>> 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 -<br>> <br><br>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?<br><br>> g_traj -f traj.trr -s pull.tpr -of force.xvg<br>> <br>> But in the force.xvg profile I am getting both positive and negative values of force. What does it mean? Please suggest.<br><br>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.<br><br>-Justin<br><br>> Samrat <br><br>-- ========================================<br><br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral
Scholar<br>MILES-IGERT Trainee<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a target="_blank" href="http://vt.edu">vt.edu</a> | (540) 231-9080<br><span><a target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><span><a target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br><span>Please search the archive at <a target="_blank" href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!</span><br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a
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