[AMBER] center of mass restraint in pmemd.cuda

From: Rajarshi Roy <phd1701171011.iiti.ac.in>
Date: Thu, 15 Mar 2018 15:37:49 +0530

Dear amber users and developers,

I am trying do an umbrella sampling of nucleic acid. One of my restraint
co-ordinate is cpd angle (pseudo- dihedral angle ), for that I need to
restraint center of mass of four group of atoms. I am little bit confuse
how to choose the iat value. In the manual I found that it should be
negative, but it is not running in cuda. Here is my restraint file,

= psu1, r2 = psu0, r3 = psu0, r4 = psu2,rk2 = 50000.0, rk3 = 50000.0,

Can anyone suggests what to do ?
Thank you in advance!
with regards
Rajarshi Roy
PhD Research Scholar
Biosciences and Biomedical Engineering
Indian Institute of Technology, Indore
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Received on Thu Mar 15 2018 - 03:30:02 PDT
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