On Thu, Apr 28, 2005, Ilyas Yildirim wrote:
>
> The previous problem I have described was not about the modification I
> have done by changing the source code. I just wanted to see the
> initial (nstep=0) energy and dv/dl results of eth->meth and meth->eth
> transformations. Theoretically, the dv/dl results for both cases should be
> equal to each other for the same lambda value (with a sign difference),
> but I have showed that this depends on the cutoff we chose. (In my case,
> I have chosen 2 cutoffs, cut=10 and cut=30. In cut=30, the expected
> result was satisfied, but for cut=10, it was not; which I could not
> explain why) But in all these test cases, I used the original sander.
You might be able to debug this in this way: Run short calculations at both
lambda=1 and lambda=0 with both prmtop files. The lambda=1 results from one
prmtop should exactly match the lambda=0 results from the other. If there are
any differences, you will have to track them down to individual interactions
that are present in one state but not in the other. You might have to print
out all nonbonded pairs involving the solute atoms; fortunately, this is a
pretty small list, so it seems likely that you could find out where the
detailed differences are. Unlike Thomas, you seem(?) to be using a
non-periodic calculation, so there may be no correspondence in the source of
the problem.
....good luck...dac
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Received on Thu Apr 28 2005 - 14:53:01 PDT
