AMBER Archive (2009)

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

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Jan 20 2009 - 14:53:48 CST

On Tue, Jan 20, 2009, Marek Mal? wrote:

>
> I am dealing with simulations of dendrimer/(RNA,DNA) complexes.
> Of course that one of the main information of the interest is free
> energy of binding including also the entropic contribution. But I
> recently found out that the entropy calculation for the bigger
> systems ( let say around 10000 atoms) is really very problematic task.

Indeed. It usually takes heroic efforts (within a supercomputer center)
to go beyond this.

> "allocation failure in vector: nh = 2159739729"

The NAB code is giving a more useful error message (rather than a
segfault). Here you are asking for 2.1 billion vector elements, each 8
bytes long, for a total of 17.3 Gbytes. How to get success in such a
request is something that depends a lot on the local environemnt.

>
> Here is whole output from NAB:
>
> ################NAB OUTPUT##############NAB
> OUTPUT####################################################
> Reading parm file (g7C_DNAds.prmtop)
> title:
>
> mm_options: cut=999.
> mm_options: ntpr=1
> mm_options: nsnb=99999
> mm_options: diel=C
> mm_options: gb=0
> mm_options: dielc=1.0
> iter Total bad vdW elect nonpolar genBorn
> frms
> ff: 0 672691.69 40992.92 8545.93 623152.83 0.00 0.00
> 3.82e+01
> ff: 1 672691.69 40992.92 8545.93 623152.83 0.00 0.00
> 3.82e+01
> ff: 2 672691.68 40992.92 8545.93 623152.83 0.00 0.00
> 3.82e+01
> mm_options: ntpr=1
> allocation failure in vector: nh = 2159739729

If/when you solve the memory problem, you will need to use xmin to
minimize to a *much* lower "frms" (force rms) value, something like
10**-5 or lower (rather than the value of 38 listed above.) See the
txmin.nab example in $AMBERHOME/test/nab, but set the value of
xo.maxiter to a much larger value (try a few thousand to begin with).

...good luck...dac

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