<br>Is the way to decompose pull force?<br><br><div class="gmail_quote">2010/10/12 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div><div></div><div class="h5"><br>
<br>
๐ลิา ๐ฯะฯื wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Hello dear gmx-users!<br>
<br>
So, I run md and got all files md.cpt, .trr, .gro, mdf.xvg,... etc.<br>
then I did: grompp_d -f sp.mdp -c md.gro -n index.ndx -p topol.top -o sp.tpr<br>
where sp.mdp differ from md.mdp in one line: energygrps = Protein SOL (in md.mdp: energygrps = System)<br>
after that I did: mdrun_d -s sp.tpr -pf spf -rerun md.trr<br>
and got file spf.xvg, but there was no forces:<br>
<br>
@ title "Pull force"<br>
<br>
@ xaxis label "Time (ps)"<br>
@ yaxis label "Force (kJ/mol/nm)"<br>
@TYPE xy<br>
0.000000 0.000000<br>
20.000000 0.000000<br>
40.000000 0.000000<br>
60.000000 0.000000<br>
80.000000 0.000000<br>
100.000000 0.000000<br>
120.000000 0.000000<br>
140.000000 0.000000<br>
160.000000 0.000000<br>
180.000000 0.000000<br>
200.000000 0.000000<br>
<br>
Also while reading frame I had a warning:<br>
<br>
WARNING: Some frames do not contain velocities.<br>
Ekin, temperature and pressure are incorrect,<br>
the virial will be incorrect when constraints are present.<br>
<br>
But I have no idea how to fix this.<br>
<br>
</blockquote>
<br></div></div>
I'll take a guess, but that's all it will be. When using mdrun -rerun with new energygrps, the only difference is the terms that are written to the .edr file. You will not get a different pullf.xvg file. The pull force between two groups is independent of the groups you've set for simple output control, anyway. That's all that energygrps will do for you - decompose nonbonded terms between the selected groups.<br>
<br>
Probably the pull code is dependent upon some of the missing terms. From the warning you get, I suspect that you didn't save velocities in the .trr file, so some energy terms will be incorrect, as you're being told. I doubt, however, that even if you had velocities, the pullf.xvg file would change.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Help me, please.<br>
<br>
Sincerely.<br>
Petr.<br>
<br>
</blockquote>
<br></div>
-- <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 href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br><font color="#888888">
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</font></blockquote></div><br>