Hi all I have been having trouble setting up a peptide+water simulation system due to the appearance of clashes in an energy minimization.
Trying to pin down the origin of the problem I have found that a minimum system that reproduces my problem is a box with multiple copies of an unblocked serine dipeptide, which I am simulating using a combination of an Amber force field and TIP3P water. I have created a gist in case anyone could please help. https://gist.github.com/daviddesancho/00b23264fed0b6d20ec4e26e7d7810e7 At some point in the minimization, the energy drops asymptotically (also, the forces become massive, ~1e+07). Surprisingly, this does not occur when the number of copies of the dipeptide is N=1, 2 or 3. The resulting minimized structure has a cycle formed by atoms in the C-terminal serine, and one of the carboxylic oxygens overlaps with the alcoholic hydrogen. So far, I have been able to reproduce this with different force fields from the Amber family and the drop in the energy seems easy to rationalize, based on the parameters. The sidechain hydrogen (HG) and oxygen (OC1) have opposite charges, while the hydrogen has 0 sigma and epsilon. Hence the interaction energy of the hydrogen will be zero and the Coulomb term will be maximized for r_OH=0. No surprise, then that they attract each other. But why do they clash only when there are 4 molecules around? I have checked different box sizes and initial configurations to no avail. Also, adding water and ions to neutralize the box and increase charge screening does not change the outcome qualitatively (although it makes the visualization trickier). As always, all help greatly appreciated, David -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.