On Tue, Jan 28, 2003, Xiang, Tian-Xiang wrote:
>
> I am conducting free energy calculation for mutating a dipeptide to a
> monpeptide (e.g. ALA-ALA -> ALA) in a box of ~900 CCL4 using gibbs. I have
> the following questions:
>
> 1. As shown below (within the dashed line), the output report file shows
> that 14EL = 0.00, 14NB = 0.0, and BADH = 0.00 while clearly 1-4 Elec etc.
> are not zero. What's happen? Have I missed something? My input file is also
> listed below.
> intprt=1,
See the manual about the intprt variable: with a value of 1, no 1-4
interactions are accumulated, which is what you are seeing.
> 2. The output report file contains many lines of " nb-update: total=
> 912973 hbpair= 0 pert= 23698", which is annoying. How can I
> supress them?
Find the place in the code where this line is printed, comment it
out, and recompile. Sorry, there's no simpler solution.
..dac
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
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Received on Tue Jan 28 2003 - 12:03:37 PST
