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AMBER Archive (2003)Subject: gibbs run
From: Xiang, Tian-Xiang (txian2_at_email.uky.edu)
Dear Sir:
I am trying to calculate free energy for mutating a dipeptide to a monpeptide (e.g. ALA-ALA -> ALA) using gibbs. According to the manual, for decoupling electrostatic constribution, two runs are needed: : electrostatic
I am not sure how these two runs can be set up. My understanding is that:
After the first run is finished, copy the restart file to be the inintial coordinate file and start the second run.
Are the above procedures correct?
T.X. Xiang
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