<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div>The crash seems to be expected as by crossing the pbc the distance will change significantly<div>and in way the algorithm can not handle. </div><div><br></div><div>Note that the overall translational motion of your system should always be removed. </div><div><br></div><div>The removal of the COM motion of your bilayer should be sufficient to prevent the overall</div><div>motion of the bilayer. have a look at the following option in the mdp:</div><div><div>; mode for center of mass motion removal</div><div>comm-mode = Linear</div><div>; number of steps for center of mass motion removal</div><div>nstcomm = 1</div><div>; group(s) for center of mass motion removal</div><div>comm-grps = membrane solvent+ions</div><div><br></div></div><div><br><div><div>On Apr 27, 2010, at 12:07 PM, ERIKSSON, EMMA wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div ocsi="0"><div style="font-size: 13px; color: rgb(0, 0, 0); direction: ltr; font-family: Tahoma; "><div><div>Hi all!</div><div> </div><div>I have a problem regarding lipid bilayer simulations in Gromacs 4. During some of my simulations the whole system is moving in the z direction in the box, meaning that after some time the lipids are going out in the bottom of the box and coming in in the top of the box, since I'm using periodic boundary conditions. This doesn't matter (I think) when running non-constrained simulations, however when I'm constraining the distance between the lipids (pull_geometry=cylinder) and a molecule in the system the system explodes and the simulations crash when the lipids are starting to cross over to the other side. The fact that the system is moving in the box must be the problem since the system explodes exactly when the first lipid passes over to the other side and nothing like this ever happens when the bilayer is not moving in the box. Is there any way to freeze the cylindrical COM of the lipids or something like that so that they stay more or less in the middle of the box all the time? I don't want to use freezegrps and freezedim = N N Y as this freezes the lipids completely in the z direction, and that's not what I want, I want them to be free to move as before but I want to stop the whole system from moving too much in the z direction. Anyone that has experienced a similar problem or know how to go about with this? I would really appreciate any help I can get. Thanks.</div><div> </div><div>Emma</div></div></div>--<span class="Apple-converted-space"> </span><br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/search">http://www.gromacs.org/search</a><span class="Apple-converted-space"> </span>before posting!<br>Please don't post (un)subscribe requests to the list. Use the<span class="Apple-converted-space"> </span><br>www interface or send it to<span class="Apple-converted-space"> </span><a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read<span class="Apple-converted-space"> </span><a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a></div></blockquote></div><br></div></body></html>