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

[ms]

On 18/10/10 13:06, Mark Abraham wrote:
> 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.

Found - mdrun0.log . It's a 4.2 Gb file (argh), I am now trying to grep 
it and see.

m.