Re: [AMBER] estimate memory requirements for

From: Jason Swails <>
Date: Mon, 11 Nov 2013 11:50:10 -0500

On Mon, 2013-11-11 at 15:52 +0100, Vlad Cojocaru wrote:
> Dear all,
> Is there a way to a priori estimate the memory requirements for an
> job given the number of atms in the system and the number
> of frames to process ?

Depends. For GB and normal modes, you can estimate it. For PB, not
really/not sure.

Given N atoms...

For GB, you need to store 3N doubles for the particle positions, another
2N doubles for the atom parameters, and then all of the data structures
necessary for evaluating the full energy. I believe GB memory
requirements should scale more or less linearly with the number of atoms
in the system (you can always plot memory usage vs. system size to see).

For normal modes, you need slightly more than 3N*3N/2 doubles to store
the upper-triangular part of the symmetric Hessian matrix in addition to
the data structures needed to evaluate the total energy (which will
scale linearly with N). The major expense here is the N^2 scaling of
the Hessian storage. (The BLAS/LAPACK routines will also need working
space in RAM to store temporary data).

For PB, on the other hand, the memory is dominated primarily by the
grid, I believe. The grid size depends as much on the shape and
compactness of the molecule as it does on its size. I am less certain
of how to estimate RAM usage here. (It also depends strongly on the grid
spacing, obviously.)

3D-RISM is similar in concept to PB in that it requires a grid. If I
recall conversations I've had with RISM experts, the 3D-RISM grid needs
to be denser than the corresponding grid for PB, so RAM requirements for
3D-RISM are typically a bit higher than PB, although I think the scaling
behavior is similar.

For a moderately large system, normal mode calculations can use between
2 and 4 GB (even more for very large systems). GB calculations I would
peg in the 500 MB range, whereas PB calculations are more in the 1-2 GB
range for large systems.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 11 2013 - 09:00:03 PST
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