[gmx-users] Regarding Torsional energetics

[Justin Lemkul]

On 10/1/12 12:43 AM, Ravi Kumar Venkatraman wrote:
> Dear All,
>               To find out gas phase torsional energetics I have restraints
> dihedral and calculated the energies. But the Dihedral restraints are not
> working properly, its changes +/- 2-5 degree from the specified value. Is
> there any other way we can run torsional energetics are I have chenge the
> modifications in the *.top and *.mdp files.
>

Restraints are simply biasing potentials; they do not fix any parameter at a 
given value.  The dihedral fluctuation is entirely normal.  If you want to 
reduce the fluctuations, increase the value of dihre_fc in the .mdp file.

-Justin

> I made following modifications in my *.top file and *.mdp file to make
> dihedral restraints.
>
> #include "dab.itp"
>
> [ dihedral_restraints ]
>
> ; ai    aj     ak    al  type  label  phi  dphi  kfac  power
>
>    26   23    18     6     1      1         0       0          1        2
>
>
>
> ;dihedral restraints
>
> dihre               = yes
>
> dihre_fc            =  100
>
> Thank you
> *
> With Regards,
> Ravi Kumar Venkatraman,
> IPC Dept., IISc,
> Bangalore, INDIA.
>
> +91-9686933963.*
>

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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