AMBER Archive (2009)

Subject: Re: [AMBER] pairwise per-residue decomposition

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Thanks for the reply!

I can complete the run considering only 3 snapshots of the trajectory,
however I can not complete the run with all 1000 snapshots.

Manoj

On Thu, Oct 29, 2009 at 6:20 AM, Carlos Simmerling <
carlos.simmerling_at_gmail.com> wrote:

> maybe you could try a test on a smaller system to see if it's really a
> memory limit.
>
> On Thu, Oct 29, 2009 at 12:34 AM, manoj singh <mks.amber_at_gmail.com> wrote:
>
> > Hi all,
> >
> > I am trying to do pairwise per-residue decomposition of MM-GBSA binding
> > free
> > energy for a protein ligand system. My calculation is crashing (the
> > computer
> > stop responding) on the "=>> Calc delta from raw data", probably due to
> the
> > memory issue. I will be very thankful if some one can tell me a fix of
> this
> > problem.
> >
> > Manoj
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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