> hi guys, > > for quite a long time i am trying to 'create' a forcefield for aliphatic > alcohols (right now, for ethanol) to use with a water potential we > employ in our simulations. > > there is a problem - the water potential uses combination rule 2, so i > thought i would just try to use FFGMX and OPLS and change it a bit. it > didn't seem to work. i also tried the FFAMBER, that uses exactly this > combination rule. unfortunately, it fails as well. > > i'm getting all sorts of errors - segfaults, lincs failures, ... in most > cases, the whole simulation 'freezes' (kinetic energy of order of 1e-5, > for example) and nothing happens. i am also quite frequently getting > close contacts between atoms (within one molecule, or between two > different molecules). > > it seems i am missing something in the forcefield, but i am not able to > identify what is it... i would be very grateful if anyone of you could > help me and shed more light in this.
To diagnose the source of this problem, you want to eliminate variables. Start with a simple system, say methanol in vacuo, and see if you can do a sensible energy minimization on that. Verify the various parts of the potential energy by hand in a spreadsheet or something. Once you're happy that your alcohol internal potentials are all good, then try an isolated water-methanol complex and repeat. Gradually increase complexity and then when something explodes you only have a few possible sources of problems. > also a 'side question' - when using FFAMBER, there are dihedrals defined > with all atom names specified (e.g., CT CT CT CT), and also dihedrals > with wildcards (X CT CT X). for a CT-CT-CT-CT dihedrals, both of these > would be applicable - are they both used in the simulation, or does the > latter (X CT CT X) override the former definition (CT CT CT CT)? I would expect that a specific atom type would override a generic atom type, although the manual seems to be silent on this issue. You can test for this in your testing scheme above, of course! Mark _______________________________________________ gmx-users mailing list [email protected] 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
