Re: [AMBER] TI in vacuum

From: FCUP <Sílvia>
Date: Tue, 1 Feb 2011 17:02:40 +0000

Hi,

yes, the simulations work in water, with no problem.
When I try to run the simulation again, it stops at the same point.
The final structure looks ok again. I attached a folder with some files.

Thanks again!

Sílvia


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

> do the simulations work in water? Do they stop at the same point each
> time, or not start at all? What does the final structure look like?
>
> Thomas
>
> On Tue, February 1, 2011 11:28 am, Sílvia Martins (FCUP) wrote:
> > 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
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> > 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.
> >
> > Sílvia Martins
> >
> >
> >
> >
> >
> > --
> > Sílvia Alexandra Pinto Martins
> > PhD student
> > Chemistry Department
> > Faculty of Sciences
> > University of Porto
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Sílvia Alexandra Pinto Martins
PhD student
Chemistry Department
Faculty of Sciences
University of Porto



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Received on Tue Feb 01 2011 - 09:30:04 PST
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