Berk, > I assume you are using a rigid water model, and thus constraints via SETTLE.
Yes, OK. > Constraining is required to measure the size of the force (for convergence > and > step size adjustment) and to make correct steps without enormous extra > displacements in the direction of the force which could cause problems due > to non-linearity. > In Gromacs 3 we had only a coordinate version of SETTLE and LINCS > did not work well for "triangle constraints". So to constrain the force > during EM > we needed to use only coordinates. The trick is to add c*f to the > coordinates, > somewhat analogous to constraining velocities in leap frog, and then get the > force without constraint components as: > (x+c*f - constrained(x+c*f))/c > I chose c as the minimization step size divided by the maximum force. > But there are two issues here, for large c non-linearity problems > and for small c float/double accuracy issues. > The non-linearity issue could be causing your problems. > Although there is also another issue: water is difficult to minimize in > general. Hmm. Is this different from how other packages handle this issue? I have never had the recurring problems with minimization in GROMACS that I have in other packages. Even though, strangely enough, water is a common feature in most of the simulations I run. I'll try and give this a shot in GROMACS 4 soon, I suppose. And I'll put together a bugzilla. Thanks, David > > > Berk. > > > ________________________________ > Express yourself instantly with MSN Messenger! MSN Messenger > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > 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 search the archive at http://www.gromacs.org/search before posting! 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