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

ms devicerandom at gmail.com
Mon Oct 18 14:01:20 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).

In gmxdump -s output I find:
functype[32]=DIHRES, label=1, power=   1 phi=-9.00000000e+01, dphi= 
7.50000000e+01, kfac= 2.00000000e+00)

which seems consistent with what I put in the topology. I looked a bit 
in the dump but it's quite difficult for me to understand what it is 
dumping and how it can be relevant.

If you need other info, the full dump, etc., let me know.


More information about the gromacs.org_gmx-users mailing list