AMBER Archive (2009)

Subject: Re: [AMBER] Question about Thermal Integration with Softcore

From: steinbrt_at_rci.rutgers.edu
Date: Wed May 13 2009 - 10:11:16 CDT

Hi Elodie,

running a TI change in which some molecule completely disappears is no
problem. See here for an example:

Steinbrecher, T. and Mobley, D.L. and Case, D.A., J. Chem. Phys., 127,
214108, 2007

however if your ion is in anisotropic surroundings, i.e. bound to
something, you may get convergence problems towards the end (high lambdas)
of your simulation and need to introduce additional restraints. Look at
e.g. Deng, Roux, J. Chem. Theor. Comput. 2006, 2, 1255-73 on one way to do
that.

You will have to run charge removal and vdw removal as two completely
independent simulations (we're working on a way to allow both in one step
for amber11). Each of these will run with two groups, so that your
starting state is on one processor group and the end state on the other.

See Amber Tutorial A9 for practical consideration on how to run such a
simulation:

http://ambermd.org/tutorials/

Kind Regards,

Thomas

On Wed, May 13, 2009 5:13 am, Elodie Laine wrote:
> Dear all,
>
> I want to perform a FEP using the Thermal Integration functionality of
> sander, with softcore. Instead of mutating my ligand (a calcium ion
> actually), I simply want to make it disappear. Do I need to run the TI
> steps (removing charges + removing vdW) on 2 processes V0 and V1, using
> the "groupfile" option, in this case ? Or can I simply simulate one
> process ?
>
> Thanks in advance.
>
> Elodie Laine
>
> Pasteur Institute
> Structural Bioinformatics Unit
> 25-28, rue du Dr Roux
> 75724 Paris Cedex 15
> FRANCE
> +33 (0)1 44 38 94 82
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

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

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