Hi Hector,<br>
<br>
You can safely ignore this. It sometimes marks the start of the system
crashing, where some groups (lysine NH3) start spinning and accumulate
energy in the spin, at a certain moment causing the system to explode.
But in your case the system recovers well from it, it seems.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br><br><div><span class="gmail_quote">On 9/22/05, <b class="gmail_sendername">Hector Mtz-Seara</b> <<a href="mailto:h.seara@qf.ub.es">h.seara@qf.ub.es</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear users,<br><br>I am simulating a monolayer system and after preparation -><br>minimization, at the beginning of the simulation I get the following<br>warning:<br>Step 1, time 0.002 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:
<br>max 0.131090 (between atoms 3748 and 3749) rms 0.002769<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br><br>After 5 of them they disappear for the rest of the dynamic. My question
<br>is if might I be concerned for that or I can Ignore them as they have<br>disappeared?.<br><br>Thanks in advance.<br>_______________________________________________<br>gmx-users mailing list<br><a href="mailto:gmx-users@gromacs.org">
gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please don't post (un)subscribe requests to the list. Use the<br>www interface or send it to
<a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br></blockquote></div><br><br clear="all"><br>-- <br>Tsjerk A. Wassenaar, M.Sc.<br>Groningen Biomolecular Sciencesand Biotechnology Institute (GBB)
<br>Dept. of Biophysical Chemistry<br>University of Groningen<br>Nijenborgh 4<br>9747AG Groningen, The Netherlands<br>+31 50 363 4336