[gmx-developers] dihedral restraints documentation

David Mobley dmobley at gmail.com
Wed Oct 5 21:45:45 CEST 2011

Just a note concerning dihedral restraints documentation -- the function and
default behavior of dihre-fc needs to be documented somewhere in the manual.
I just spent a couple hours (and my student a couple of days!) trying to
track down the source of some crashes which ended up being due to the
difference between specifying

dihre-fc = 1

in our topology file, and not specifying anything at all.

THis how-to documents what dihre-fc DOES (
http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints) but it is
not mentioned anywhere in the gromacs manual at all. It turns out dihre-fc
defaults to 1000, so the difference between dihre-fc = 1 and omitting
dihre-fc is a factor of 1000 in dihedral restraint strength. This is enough
(since it's a multiplier!) to make the difference between simulations
reliably crashing and simulations not crashing at all...

This clearly should be documented in the manual since (with this behavior)
knowing what value of dihre-fc one is using is critical to knowing what
dihedral restraint strength one is using.


David Mobley
dmobley at gmail.com
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20111005/775095ad/attachment.html>

More information about the gromacs.org_gmx-developers mailing list