[gmx-developers] Re: [gmx-users] dihedral restraints documentation
Mark.Abraham at anu.edu.au
Thu Oct 6 13:57:07 CEST 2011
On 6/10/2011 6:45 AM, David Mobley wrote:
> 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.
Thanks for the report. I have noted this need in a Redmine documentation
issue for 4.5.6.
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