[AMBER] ¡¾amber¡¿center of mass&umbrella sampling

From: whb <wwwhbpt.gmail.com>
Date: Fri, 6 Jun 2014 15:11:40 +0800

Dear amber users£º

         I want to know that the dimer-to-monomer transition of a protein by
using CPHMD simulations and the umbrella sampling method to obtain the
potential of mean force(PMF) as a function of the distance between the
centers of mass of the two monomers.

Now I have a little trouble writing the DISANG file. Monomer has 79AAs. I
don¡¯t know how to acquire the original distance between the two monomers,
and don¡¯t know how to define the distance between two residues. I tried to
read the manual, but still got a little problems. I hope someone could help
me finish the DISANG file. And tell me how to define the variable number.



r1=0.0, r2=10.0, r3=10.0, r4=100.0,

rk2 =1.0, rk3 = 1,






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Received on Fri Jun 06 2014 - 00:30:02 PDT
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