<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>Hi Justin,<br>I the pullf.xvg file also, some values are negative. I am giving below the pull code -<br><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;">pull = umbrella<br>pull_geometry = distance<br>pull_dim = Y Y Y<br>pull_start = yes <br>pull_ngroups = 1<br>pull_group0 = freeze<br>pull_group1 = pull<br>pull_rate1 = 0.01<br>pull_k1 = 1000<br><br>I have given pull_dim Y Y Y as I am not pulling in a particular direction. Is it
right?<br><br><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Samrat Pal <psamrat10@yahoo.com><br><b><span style="font-weight: bold;">To:</span></b> jalemkul@vt.edu; Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Sat, August 14, 2010 11:00:37 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] negative values of force<br></font><br>
<meta http-equiv="x-dns-prefetch-control" content="off"><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div>Thanks a lot.<br>Best<br>Samrat<br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><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> Gromacs Users' List <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Sat, August 14, 2010 10:50:05 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>> (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><br>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.<br><br>> (2) So, there is no error in getting the negative value of force, right?<br>> <br><br>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.<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><br>Again, the actual pull output (pullx.xvg) should be a suitable match for your pullf.xvg data.<br><br>-Justin<br><br>> Best<br>> Samrat<br>> ------------------------------------------------------------------------<br>> *From:* Justin A. Lemkul <<a rel="nofollow" ymailto="mailto:jalemkul@vt.edu" target="_blank" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>> *To:* Discussion list for GROMACS users <<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>> *Sent:* Sat, August 14, 2010 10:34:25 AM<br>> *Subject:* Re: [gmx-users] negative values of force<br>> <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 rel="nofollow"
target="_blank" href="http://vt.edu">vt.edu</a><span><span> <<a target="_blank" href="http://vt.edu">http://vt.edu</a>> | (540) 231-9080</span></span><br><span><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></span><br>> <br>> ========================================<br>> -- gmx-users mailing list <a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a> <mailto:<a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br><span><span>> <a target="_blank" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span></span><br><span><span>> Please search the archive at <a target="_blank"
href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!</span></span><br>> Please don't post
(un)subscribe requests to the list. Use the www interface or send it to <a rel="nofollow" ymailto="mailto:gmx-users-request@gromacs.org" target="_blank" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a> <mailto:<a rel="nofollow" ymailto="mailto:gmx-users-request@gromacs.org" target="_blank" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>>.<br><span><span>> Can't post? Read <a target="_blank" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></span></span><br>> <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]vt.edu | (540) 231-9080<br><a rel="nofollow" target="_blank"
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