[AMBER] Tools to calculate free energies landscape from the MD simulation without doing PMF?

From: Catein Catherine <askamber23.hotmail.com>
Date: Fri, 25 Mar 2011 16:13:33 +0800

Thank you All who tried to help.
Yes. Thomas. It is what I meant.
I am trying to analysis the free energies landscape for a protein. I have done 20ns simulation for the system. The RMSD, energies, etc are converged.
Could you mind to let me know the command used in ptraj to calculate the histogram P(x)? Once we got the P(x), should we use wham or any other program to calculate the dF=-RTlnP(x)?
Best regards,
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Received on Fri Mar 25 2011 - 01:30:03 PDT
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