<html><body><div style="color:#000; background-color:#fff; font-family:times new roman, new york, times, serif;font-size:12pt"><div><span>OK, thanks.</span></div><div><span>But may these lines in md.mdp file change the result and solve the problem?</span></div><pre>; COM motion removal
; These options remove motion of the protein relative to the solvent/ions
nstcomm = 1
comm-mode = Linear
comm-grps = Protein_Water </pre><div> </div><div>Sincerely,<br>Shima<br></div> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div style="font-family: times new roman, new york, times, serif; font-size: 12pt;"> <div dir="ltr"> <font face="Arial" size="2"> <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> Shima Arasteh <shima_arasteh2001@yahoo.com>; Discussion list for GROMACS users <gmx-users@gromacs.org> <br> <b><span style="font-weight: bold;">Sent:</span></b> Sunday, June 17, 2012 7:00 PM<br> <b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] Strange behaviour of bonds<br> </font> </div> <br>
<br><br>On 6/17/12 10:23 AM, Shima Arasteh wrote:<br>> Hi all,<br>><br>> I simulated a protein in water. When I get its 20 ns trajectory and load it in<br>> VMD, I see some bonds stretch suddenly and moves far strangely! Is this problem<br>> because of the wrong structure of the protein? Or I may put some restrains on<br>> system and solve this problem?<br>> Anybody may suggest me in this about?<br>><br><br>Please read this page in its entirety:<br><br>http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions<br><br>-Justin<br><br>-- <br>========================================<br><br>Justin A. Lemkul, Ph.D.<br>Research Scientist<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>http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br><br>========================================<br><br><br><br><br> </div>
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