Re: [AMBER] TI in vacuum

From: <>
Date: Tue, 1 Feb 2011 09:46:03 -0500 (EST)

> However, with some compounds, the vacuum simulations stop, without any
> error
> message. This occurs in step2, when hidrogen disappears while
> simultaneously
> the hydroxyl group appears.
> What could be the problem?

hm, you are not giving that much information about the problem, so its not
easy to say anything beyond the fact that in principle, TI should work in
vacuum as well. Do your simulations stop at the same point each time? Do
you see anything in the structure when you write out the trajectory? Did
you check both output files for errors (sometimes a message only appears
in v0.out or v1.out)



Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Tue Feb 01 2011 - 07:00:04 PST
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