<div>Dear all, Thanks for all comments. I will check again all steps for my previous simulation with right files (according to Mark) and then I will let you know if I got the same problem (I am not working on proteins).</div>
<div>Another question: </div>
<div>--After energy minimization step for in-vacuo run, Should I do still position restrained MD, since I want the bond length be fixed (constraints=all-bonds)?</div>
<div>--After pr-md in mdrun step for in-vacuo simulation, is it true that I will get the movement of my molecule in vacuum?? I appreciate your help/Jamie<br><br></div>
<div class="gmail_quote">On Wed, Aug 12, 2009 at 3:53 AM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi,<br>
<div class="im"><br>On Wed, Aug 12, 2009 at 3:06 AM, Mark Abraham<<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>> wrote:<br>> Jamie Seyed wrote:<br>>><br>>> Dear all,<br>>> I performed an md simulation but it crashed at the beginning because<br>
>> according to it "system was exploding". Also when I tried to see the<br>>> system<br>>> by ngmx, there was no water anymore and it was only the molecule sitting<br>>> in<br>>> the box(after grompp and before mdrun it was a box of water plus the<br>
>> molecule)!!??<br>><br>> So you used a wrong file at some point... name your files carefully, and use<br>> them carefully.<br><br></div>Maybe xtc-grps was set to "protein"? That wouldn't be related to the<br>
problem. But did the crash occur directly, at step -1/0/1, or did the<br>system run at least for a few steps? What exactly were you doing?<br>Please copy-paste your command lines, your .mdp file and the mdrun<br>output (not the log file yet, please).<br>
<br>Cheers,<br><br>Tsjerk<br><br>--<br>Tsjerk A. Wassenaar, Ph.D.<br>Junior UD (post-doc)<br>Biomolecular NMR, Bijvoet Center<br>Utrecht University<br>Padualaan 8<br>3584 CH Utrecht<br>The Netherlands<br>P: +31-30-2539931<br>
F: +31-30-2537623<br>
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