Re: Problems about FEP simulation

Date: Fri May 21 2010 - 14:52:53 CDT

Generally this occurs due to the cutoff distance.
I would suggest this:
1] Measure the dimensions of the system using "measure" command
2] Use slightly higher values than your actual dimension for cell basis
3] Use slightly smaller values for cavity size than the actual size of the
cavity. If these values ( ~12 by 20 by 24 A) are approximate then OK

I hope this might work


> Dear All,
> I am Yang Gao, from Iowa State University. Recently, I am conducting some
> FEP simulation to calculate water energy in a big cavity. The dimension of
> the cavity is somewhat big, ~12 by 20 by 24 A. In the simulation setup,
> each
> water is gradually replaced with a DUMMY atom. The problem is whenever I
> did
> minimization for the FEP system, I will get the "bad global exclusion
> count"
> error. I have checked the psf file and seems the exclusion list in it is
> good. Later I noticed this problem could be that my water are far away
> from
> each other (could be as far as 24 A). So I enlarge the cutoff to 24, and
> the
> error disappeared.
> So my question here is: First, could this cutoff be the reason for the
> "bad
> global exclusion count" error? If so, is there any other way to solve this
> problem other than bigger cutoff? And then will this big cutoff be a big
> problem besides making the simulation slow?
> I really appreciate any help or suggestions. Thank you very much.
> Yang

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