Hi Jones, Did you first try the readily available C6? I would not suspect any problem with C8/9/... To me, the fact that you run into segfaults suggests that you got the topology wrong, or you're doing something wrong with setting up the system. I assume you did perform energy minimization and position restraint MD. You should be able to take the same strategy for C8/9/... as you would for C6 (for which you know that the topology is correct).
Don't try to fight symptoms, try to find the source. Cheers, Tsjerk On 3/13/07, Jones de Andrade <[EMAIL PROTECTED]> wrote:
Hi all. first, thanks a lot! :) Pedro: I've already expanded the box increadibly much (say, 200 angstrons in each direction), and the problem still remains. I mean, expanded it from an original box with size to fit the experimental density. Low temperatures where already tested in the C9 but not in the C8, I'll try later. I've tried 98.15K for 200ps, but at the moment I don't quite remember if it blowed at that temperature or when I tried to increase it. Will try again later and let you know. David: I really haven't thought about this option. I'll try later, but isn't it a dangerous behaviour such high pressure and low equilibration time at same time? Thank's a lot, any other clue will be also very thankfull. I'll test those today or tomorrow and let you know. But really thanks in advance. :) Sincerally yours, Jones On 3/13/07, David van der Spoel <[EMAIL PROTECTED]> wrote: > Pedro Alexandre de Araújo Gomes Lapido Loureiro wrote: > > Hi Jones, > > > > > > Another option is to begin the simulation at very low temperatures and > > increasing it at, say, every 500 ps. > > But it seems that your starting configuration has some problem, maybe > > too high a density? > > Comparing with the experimental value, how is your density? > > > > Regards. > > > > Pedro. > > > > > > Another related strategy is to first simulate a single molecule in a box > of say 2 x 2 x 2 nm, then use genconf to multiply the conformation to > the desired number (this way there is no overlap) and then simulate at > high pressure to shrink the box again. Finally equilibrate at normal > pressure. > > -- > David. > ________________________________________________________________________ > David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: 46 18 471 4205 fax: 46 18 511 755 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
