Hi Kirtana,
On 16/02/2012, at 11:34 AM, kirtana S wrote:
> Dear Amber Users,
>
> I want to do umbrella sampling to obtain the potential of mean force with
> distance between the residues as the reaction cordinate. The example
> discussed uses dihedral restraints. Should I use distance restraints by
> keeping one residue fixed.Please suggest .
Are you using sander or PMEMD for your simulation? if sander, and you can choose two atoms to use as the ends of the reaction coordinate instead of two residues, you can implement a distance directly, as for example in this &rst specification between atoms 1 and 7:
&rst
ixpk= 0, nxpk= 0, iat= 1, 7, r1= 0.00, r2= 2.65, r3= 2.65, r4= 18.00,
rk2=100.0, rk3=100.0, ir6=1, ialtd=0,
&end
Hope this helps,
Ben
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Received on Wed Feb 15 2012 - 15:00:02 PST
