Interesting idea, but multiple different start points have failed with PR, and succeeded with normal MD. Freeze groups seem to be working OK, so I'm using that for now - after all, it doesn't need to be 'real', I just want to equilibrate the lipid/solvent without moving my carefully-placed peptide. Interestingly, I've had similar problems before, but only when I use multiple peptides. Might try merging the chains and see what that does. I used CG with steep every 50 steps... sounds weird I know, but it's proved pretty reliable.
--- Steffen Wolf <[EMAIL PROTECTED]> wrote: > Alan Dodd wrote: > > No, minimisation was without PR. Surely > minimisation > > with PR would *increase* bad contacts, rather than > > removing them? I've tried running for a while > under > > normal MD, successfully and without LINCS errors, > then > > taking the endpoint and running under PR, but it > still > > crashes almost instantaneously, so it's unlikely > to > > just be a matter of energies or bad contacts, I'd > have > > thought? > > > > > Yes, so it looks that minimization ended at a > metastable point, which > was surmounted by a free MD run but kept by the PR > and therefore caused > the system to crash. Which minimization algorithm > did you use? Steep or CG? > > -- > Dipl.-Chem. Steffen Wolf > Department of Biophysics > University of Bochum > ND 04/67 > 44780 Bochum > Germany > Tel: +49 (0)234 32 28363 > Fax: +49 (0)234 32 14626 > E-Mail: [EMAIL PROTECTED] > Web: http://www.bph.rub.de > > _______________________________________________ > 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 > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ 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
