On Mon, Jan 27, 2003, Xiang, Tian-Xiang wrote:
>
> 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
> LAMBDA = 1 -> 0 with LAMBDA(vdw) = 1, followed by van der Waals LAMBDA = 1
> -> 0.
>
> I am not sure how these two runs can be set up. My understanding is that:
> in the first run, set ielper=1, almda=1.0, all others are set the same as a
> regular run without decoupling; in the second run, set ielper =-1,almda=1.0,
> all others are set the same as a regular run witht decoupling.
>
> 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?
The above sounds correct, assuming that the "real" molecule is the non-pert
molecule, and the monopeptide (with dummy atoms) is the "pert" molecule.
Note that almda=1.0 is the default.
..good luck....dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
10550 N. Torrey Pines Rd. | home page:
La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Mon Jan 27 2003 - 10:38:13 PST
