AMBER Archive (2009)

Subject: Re: [AMBER] Problem with entropy calculation of bigger system using NMODE and NAB.

From: David A. Case (
Date: Sat Jan 24 2009 - 08:37:31 CST

On Wed, Jan 21, 2009, Marek Mal? wrote:
> B)
> Some hope provide me the fact that NAB could be now implemented also
> in parallel version. If I run NAB on 2 empty nodes, I have 2x16GB of
> shared memory which could solve my problem, of course only in the case
> that each node do not require copy of the whole dataset. I cannot verify
> this now since in this moment I have only serial version installed, so
> eventual preliminary comments from the erudite person are welcomed !

This sounds good if you have the hardware. Use the -openmp option when
you configure AmberTools.

> C)
> The last possibility in this story is probably calculation of the entire
> system using some "per partes" approach
> or to approximate the whole entropy by some most important contribution
> ("partial entropy").

This also sounds good, although there is no general procedure. Remember
that you will always be looking at some thermodyanmic cycle, so it is
changes in entropy that matter. If there is some mostly-invariant part
of the system, you might be able to leave that out of the calculation.
Whatever you do, don't expect high precision from these sorts of

> If I use recommended approach (= enthalpic contribution with mm_PBSA
> where for E_desolv use PB model and NAB use only for the
> calculation of the entropic contribution) it is probably appropriate to
> use in NAB nonzero value for gb although previous calculation
> was carried out using PB model.

I agree. Your only options for normal modes are GB or vacuum. GB
should be closer to PB than vacuum.

> For example if I tell you "I am simulating big dendrimer (spherical
> shape) with 21 base-pair siRNA, where strongly dominate
> electrostatic interaction (positively charged dendrimer and negatively
> charged siRNA)" is it clear which gb model could be
> the most suitable for this case ?

Only gb=1 has been tested much for nucleic acids, and only gb=1 is
available for normal modes. So, your choices are pretty limited!


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