AMBER Archive (2007)

Subject: Re: AMBER: Limitation in number of atoms/residues

From: Robert Duke (rduke_at_email.unc.edu)
Date: Fri Jun 22 2007 - 07:37:30 CDT

Hi Sascha -
Are you using sander or pmemd? Are you using amber 9? For pmemd, the atom
limit should be 999,999, which is currently a limitation imposed by the
field length of the atom count in the inpcrd file, if memory serves. There
should not be a residue limit per se, except at the low end (ie., you need a
certain number of residues if you do a parallel run - you are not going to
have problems with this). For pmemd, there is also a limit on how big the
periodic box can be, based on the maximum fft grid size in any dimension.
Currently this (grid_hi, an integer parameter) is set to 256 in
mdin_ewald_dat.fpp. It can be bumped up to 512 without problems, especially
if you do parallel runs or have lots of memory. I do not know of errors in
the truncated octahedron code in tleap in amber 9 - the developers for that
code can address those issues. However, I have made a solvated orthogonal
box full of protein/tip3p water with 900,000+ atoms using amber 9 xleap,
visualized in xleap (no problems, kind of slow in xleap though; I was using
a RHEL 4 box, dual intel 3 ghz processors, 2 GB RAM). I know there can be
problems with visualizing truncated octahedra - another thing for someone
else to comment on. Bottom line - with pmemd and xleap, amber 9, using
orthogonal unit cell, the current real limit in system size is 999,999
atoms. You will definitely want to run pmemd, as sander will be really slow
on a system of this size, and you will probably want to use at least 8
processors (I did the setup runs for this system on 4 processors with
pmemd). Run times for systems in the range of 20K-1M are roughly a linear
function of system size (double the atoms, you double the run time for a
given number of steps).
Regards - Bob Duke

----- Original Message -----
From: "Sascha Rehm" <SaschaRehm_at_gmx.de>
To: <amber_at_scripps.edu>
Sent: Friday, June 22, 2007 6:47 AM
Subject: AMBER: Limitation in number of atoms/residues

> Hi all,
>
> is there still a restriction in the maximum number of atom or residues?
> I found some answers to the same question in the year 2002 (max
> atoms:99999, max res:9999), but I didn't find anything newer.
>
> If I solvate a big system with 8 proteins in tleap with water (TIP3PBOX
> and solvateoct), one edge of the octaeder ist cut off and there also is
> a part where it seems to have twice as much water as it should have.
>
> If I reduce my system from 8 proteins (after solvation about 105000
> residues and 330000 atoms) to 6 proteins (say 96000 residues) everything
> works fine.
>
> thanks for your answers
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