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

ms devicerandom at gmail.com
Mon Oct 18 13:53:36 CEST 2010

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.


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