Most WHAM programs assume a restraint pre-factor of 1/2. The AMBER
nmropt module, however, does not. Therefore you should multiply most
force constants by 2 in the metafile.
Also, angle and dihedral force constants are specified in
kcal/mol-rad^2, while the WHAM code usually assumes it is in the same
units as the coordinate values (i.e. degrees). Therefore you also need
to convert those force constants to kcal/mol-deg^2.
Cheers,
Brian
On 05/29/2015 09:46 AM, MOHD HOMAIDUR RAHMAN wrote:
> Dear all,
> I am doing Umbrella sampling with distance restrain.
> r1=0, r2=0.9,r3=0.9,r4=5
> while analyzing it by wham , I am facing a problem in defining force
> constant in meta.dat file.
> I had used rk2=30,rk3=30
> What will be the right force constant for this rk value.
> Thanks
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
--
Brian Radak
Postdoctoral Scholar
Gordon Center for Integrative Science, W323A
Department of Biochemistry & Molecular Biology
University of Chicago
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
email: radak.uchicago.edu
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Received on Sat May 30 2015 - 11:30:03 PDT
