Greetings everyone!
After trying my same shell scripts on another computer, using single
precision, I have worked out that the double precision version of
Gromacs-3.3.1 does not energy minimize consistently. The exact same run
script using different force fields will energy minimize sometimes, but
most force fields give infinite forces. This was verified for
diglycine, trialanine, alanine dipeptide as well as a very large
protein. In fact, the exact same run script for diglycine gives
minimization within 8 steps for single precision, where with double
precision it had infinite forces (for no reason) in step 0. I even
wrote a quick script to determine the nearest neighbors for each atom,
and found that all atoms were at least 0.9 Angstrom apart (so no
overlap).
Recompiling the exact same source code in single precision on my own
machine reproduced the success identically. Thus I am left to believe
that there is bug in the double precision version of the energy
minimization (mdrun_d or grompp_d, I don't know) code.
Just thought I would let everyone know to avoid double precision when
running energy minimization.
Thanks for all your suggestions!
Justin
_________________________________________________________________
Justin M. Shorb Phone: (608) 262-0483
Skinner Group [EMAIL PROTECTED]
University of Wisconsin-Madison, Department of Chemistry
1101 University Ave., Madison, WI, 53706
_______________________________________________
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
