[gmx-users] The trouble with dihedral restraints: frozen peptide backbones
Mark.Abraham at anu.edu.au
Mon Oct 18 14:06:49 CEST 2010
On 18/10/2010 10:53 PM, ms wrote:
> On 18/10/10 03:30, Mark Abraham wrote:
>>> To enforce chirality in such a toy, I thought that a simple
>>> (naive?) but functional idea could be that of enforcing a not-
>>> too-hard and wide-bottomed dihedral restrain on the phi angle,
>>> like that:
>>> [ dihedral_restraints ]
>>> ; ai aj ak
>>> al type label phi dphi kfac power
>>> ; phi C'(n-1) - N - CA - C'
>>> 5 7 8 1 1 -90 75 2 1
>> Try mdrun -debug on a short run. What does it have to say about the
>> parameter values for this dihedral restraint? Likewise gmxdump -s on
>> the .tpr (though you will have to search around for F_DIHRES among
>> other things, probably).
> I have run a 500 ps run with -debug on, but I am unsure of where
> should I look for what it says of relevance -I see the ctab,rtab,dtab
> xvg's but I doubt they are of interest.
There should be a much larger .log file, probably named differently.
Check what it reports about dihedral restraints - text searching will be
your friend, here.
More information about the gromacs.org_gmx-users