Justin,<br><br>Thanks again for attention to my problem.<br><br><br>I've checked my system and found that the problem was exactly in the 1388 atom ( wich is not properly minimized in accordance to the log files). This atom is the Cb atom of Gln residue wich placed between one loop of the protein and docked alpha helix of the peptide. Theš surrounding of that atom ( It's likely that other intracellular loops of the receptor as well as long N term protect this side chain to rotate during the minimisation ). When I've checked pdb files produced by exploding system I've found that some atoms ( from that loops) were moved from the pereodic boundaries ( I've obtain very big system as the conseqyence surrounding by some single atoms. So it all look like as big artifact :) )<br>
<br>So it seems that I need to use slightly different initial conformation of the receptor because minimisation could not to resolve such crushes.<br><br><br>Thanks again<br><br><br>James<br><br><div class="gmail_quote">1 ÁÐÒÅÌÑ 2012šÇ. 21:37 ÐÏÌØÚÏ×ÁÔÅÌØ Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> ÎÁÐÉÓÁÌ:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im"><br>
<br>
James Starlight wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Justin,<br>
<br>
Sorry again for the delay.<br>
<br>
I've finished minimise my system with the CG algorithm in double precision ( after steep minimisation )<br>
but the output was<br>
<br>
Stepsize too small, or no change in energy.<br>
Converged to machine precision,<br>
but not to the requested precision Fmax < 0.1<br>
<br>
Than I've tried to equilibrate this system with the NVT conditions and obtain old error about collapse of my system :)<br>
<br>
šI've found logs of both minimisation ( the step minimisation log was very big I've coppied only end part of this output data ) šand attach it to this topic.<br>
<br>
</blockquote>
<br></div>
Both of these log files indicate that EM was likely fine. šFor future reference, the following sections were all I was asking for all along:<br>
<br>
>From CG:<br>
Potential Energy š= -5.96597537065782e+05<br>
Maximum force š š = š1.42815783701700e+02 on atom 1388<br>
Norm of force š š = š1.58963638409829e+00<br>
<br>
>From steep:<br>
Potential Energy š= -5.7233788e+05<br>
Maximum force š š = š7.0209003e+02 on atom 1388<br>
Norm of force š š = š1.1310696e+01<br>
<br>
CG gives you the better minimization, overall, as expected. šAtom 1388 bears the maximum force, but it is not of problematic magnitude.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Also I've run minimisation in vacuum as you've told me but this results would be aviable tomorrow.<br>
<br>
</blockquote>
<br></div>
It's probably not necessary, after all. šI was guessing at that point based on incomplete information.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Could you tell me whats exactly wrong with that system and is there possible ways to fix the problem?<br>
<br>
</blockquote>
<br></div>
As I've said before, the only strange thing you seem to be doing is with your comm-grps. šChange this setting to "System" and see if it runs. šOtherwise, I can find no reason for the immediate instability. šIf it still crashes, perhaps decrease the time step for the initial equilibration.<div class="HOEnZb">
<div class="h5"><br>
<br>
-Justin<br>
<br>
-- <br>
==============================<u></u>==========<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.<u></u>vt.edu/Pages/Personal/justin</a><br>
<br>
==============================<u></u>==========<br>
-- <br>
gmx-users mailing list š š<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/<u></u>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/<u></u>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/<u></u>Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br>