Re: [AMBER] TI in vacuum

From: FCUP <Sílvia>
Date: Tue, 1 Feb 2011 16:28:14 +0000

The compounds are, for example, Imidazole-->Imidazole-5-ol or
Purine-->Purine-8-ol.

2011/2/1 <steinbrt.rci.rutgers.edu>

> > 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)
>
> Regards,
>
> Tom
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
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>

Hi Tom,

thanks for the quick response.
I can say that this happened,for instance, with these two transformations:
Imidazole-->Imidazole-5-ol or Purine-->Purine-8-ol.

Do your simulations stop at the same point each time?
Did you check both output files for errors (sometimes a message only appears
in v0.out or v1.out)


In the two examples, in the first one, it stops at lambda=0.4, because the
v0 stops - with no error message - and v1 terminates normally.
With this, a coordinate file (.rst file) is written for v1 but not for v0
and the calculation stops.
In the second transformation, it stops at lambda=0.1, and the v0 stops with
no error message and v1 terminates normally, again.

Do you see anything in the structure when you write out the trajectory?

I am not writing a trajectory file for each lambda. For each lambda, i am
just writing a coordinate file that corresponds to the last structure.
With this, for v0, I have a coordinate file for lambda=0.3 that seems ok.

Thanks again for your help.
I am available for further explanation if necessary.

Slvia Martins





-- 
Slvia Alexandra Pinto Martins
PhD student
Chemistry Department
Faculty of Sciences
University of Porto
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Received on Tue Feb 01 2011 - 08:30:10 PST
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