Dear GMX-community, I'm running four related, equilibrium-dynamics simulations of a small protein in explicit water, each with a different non-natural amino-acid in the sequence. One of the four non-natural amino-acid containing proteins can be simulated for long times, up to 4 ns without incident, but the other three invariably crash. On repeated reinitialization (changing the box size, changing the duration of position restrained refinement) they still keep crashing at any time between 100's of picoseconds and 2 ns. Usually an error such as "3009.270 ps: Water molecule starting at atom 26883 can not be settled." is printed to the log file and the pdb of the step after the crash has nonsense numbers for the coordinates of the offending water molecule. It's always a different water molecule, always a high-numbered atom (>20000). The crashes happen on both a self-compiled linux build and on a self-compiled Mac OS 10.4 build, both GMX 3.3.1. A simulation of just the parameterized amino acids in a box of water never crashes over the course of a 4 ns simulation so I don't suspect my amino-acid parameters.
I'm using ffamber99 and I parameterized the amino acids myself using antechamber and amb2gmx. I'm using ffamber_tip3p. Thanks for reading. -Aaron _______________________________________________ gmx-users mailing list [email protected] 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
