All, Earlier, I wrote about how I ran a large set of small molecules using GAFF parameters and all of my small molecules with triple bonds (nitriles, pentyne, propyne, etc) were crashing. This was not a parameter problem, and not a timestep problem, and, perplexingly, only seems to occur for these molecules when they are in vacuum or water, but not in a binding site.
As it turns out, we (John Chodera, Chris Fennell and I) have now traced the problem back to problems with the angles, and in particular, how GROMACS handles angle bending for nearly linear molecules. These molecules, since they have triple bonds, are basically linear, of course. Anyway, as it turns out, all of these molecules have one or several angles with preferred angles of nearly pi (or 180, whichever units you prefer). As it turns out, the angle bending code apparently can't handle angles of exactly 180 degrees, which causes the problem. This also explains why these molecules are OK when run in a binding site: The binding site bends the angle so it isn't 180. In gmxlib/bondfree.c, the relevant algorithm (in pseudocode) is something like this (where x_i, x_j, and x_k are atom vectors): t_1 = x_i - x_j t_2 = x_k - x_j cos_theta = dot(t_1, t_2) / (|t_1| |t_2|) theta = inverse_cosine(cos_theta) V = (1/2) K (theta - theta_0)^2 Now, if theta_0 is anywhere near pi, this obviously isn't going to work if inverse_cosine is defined on the domain [-pi,+pi). Hence, the problem we're seeing. The solution is simple, as John points out to me: shift this inverse_cosine domain to cover a range of [-pi,+pi) around theta_0. Then only in the (extremely rare) case that a molecule is so strained that it is pi away from its preferred value would there be instabilities. I will also submit a bugzilla. Thank you, David Mobley UCSF http://www.dillgroup.ucsf.edu/~dmobley _______________________________________________ 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
