wurl wrote: > thanks David, > i mean i always met with problems simulating amorphous and crystalline > systems without bond constraints, your suggestion of reducing the time step > is very reasonable, and i don't know a compressibility of 1e-6 will be > suitable for a polyethylene crystal cell?
Consult literature here. > and i have also not succeeded in simulating such systems with > constraints= all-angles, it always makes long warnings during the md process > and stop soon. my time step is 1fs, the oplsaa force field, and the version > is gromacs3.3 with pme.c updated. do i need to make specific changes to the > default run perameters for systems with all angles bonds constraint? LINCS (the default constraint algorithm) is not suitable for structures that require "coupled constraints", including cases of constrained angles between constrained bonds and possibly constrained angles with common bonds. Read the manual for details. Try SHAKE. 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
