[gmx-users] The trouble with dihedral restraints: frozen peptide backbones

[Mark Abraham]

  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'
>>>    3
>>> 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.

Mark