<div>Hi Jones,</div>
<div> </div>
<div> </div>
<div>Another option is to begin the simulation at very low temperatures and increasing it at, say, every 500 ps.</div>
<div>But it seems that your starting configuration has some problem, maybe too high a density?</div>
<div>Comparing with the experimental value, how is your density?<br> </div>
<div>Regards.</div>
<div> </div>
<div>Pedro.<br> </div>
<div><span class="gmail_quote">2007/3/13, Jones de Andrade <<a href="mailto:johannesrs@gmail.com">johannesrs@gmail.com</a>>:</span>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Hi everybody.<br><br>I would like to ask one question, basically about equilibration of<br>long and flexible alkyl chains.
<br><br>I'm having terrible problems in equilibrating C8 and C9 chains. I've<br>already expanded a lot the box size, but I always fall into<br>segmentation faults. Also tried smaller time steps (my "standard" is
<br>2fs), doesn't work. Reduction of the rcoulomb, rvdw and similar yields<br>some more steps, but also terrible slower simulations (too much of the<br>electrostatic calculations falling into the reciprocal part).<br>
<br>Moreover, in the minimization step, I've tried all the algorithms<br>available for minimization. None of them yields real success.<br><br>Did anybody successfully equilibrated systems like those, or similar<br>ones like n-octanol? Could anyone please give me some advice on this,
<br>any extra "trick" I forgot or don't know to try to make these<br>molecules run?<br><br>Thanks a lot in advance for any help!<br><br>Sincerally yours,<br><br>Jones<br>_______________________________________________
<br>gmx-users mailing list <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>Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php
</a><br></blockquote></div><br>