All, I may be in a hole of my own digging, here, but I've been trying to simulate a large set of small molecules in explicit solvent. I'm using the Amber GAFF parameters, converted over to GROMACS using our amb2gmx.pl script.
The problem I'm running into is that for anything with a triple bond (i.e. propyne), I get "blowing up", even in vacuum (i.e., I get a series of constraints warnings finally ending in a crash). This is with a 2 fs timestep. Since of course things with triple bonds have larger spring constants, I have tried reducing the timestep, but still run into problems with timesteps as small as even 0.5 fs, which is ridiculous, especially since the spring constants are not THAT much bigger. This made me suspect some sort of problem with the conversion script with respect to triple bonds, so I went through and hand-checked all of the bond, angle, and torsion parameters. Everything appears fine, in that manual conversion from the GAFF values gives me the same values the script is giving me. I should mention that, if I run these simulations in AMBER, even with 2 fs timesteps, I don't have any problems. Anyone have any thoughts? I'm a bit at a loss about what else to look at, here. One other thing I notice -- which, again, doesn't appear to cause any problems in AMBER -- is that GAFF specifies a dihedral force constant of zero for the c1-c1-c3-H dihedral in propyne, which means that the methyl can rotate rapidly. This doesn't appear to cause any problems in AMBER, but I do notice that the LINCS warnings I get relate to constraint deviations between c3 and H. Any ideas will be appreciated. Thanks, David _______________________________________________ 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