Hi Justin,
Double precision energy minimization works great for us, so if you
have system where you think there _might_ be a bug, please submit it
to bugzilla.
In fact, you should always use double precision l-bfgs mimimization
prior to normal mode analysis, IMHO...
Cheers,
Erik
On Apr 20, 2007, at 9:02 PM, Justin M. Shorb wrote:
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
_______________________________________________
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
