RE: AMBER: sander error

From: Ross Walker <>
Date: Tue, 18 Oct 2005 07:23:18 -0700

Hi Yam

> The system contains about 1.4M atoms with octahedron
> water and ions. And the attempting minimization is
> only step no. 1, therefore setting ntx=1 (default)
> (not even on MD runs). I have checked the last line of
> my inpcrd file and is clear that the water box is
> octahedron.
> Anyone has any idea on what is going on? could it be
> the limited number of atoms in sander? Please help.

This is a huge system, read at least an order of magnitude larger than what
we would consider a very large system. I don't think sander has even been
tested with a system this large. The errors you are getting are almost
certainly due to the system size, possibly a memory error due to some
routine not expecting such a large system and not having a big enough
buffer. E.g. reading of the prmtop file or inpcrd file etc...

You could try pmemd, this is designed to handle large periodic systems but
1.4 million atoms may be larger than this was ever tested for. Note, with
this sort of size system you are going to need some serious computing power
(> 128 cpus of a SMP machine) to have a chance of doing simulations long
enough to get meaningful results. Even then you will burn a LOT of cpu time.

I suggest you try looking at a subset of the system and just run some
simulations on that and see if you can confer any macroscopic information
from this.

All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- |
| | PGP Key available on request |

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Received on Tue Oct 18 2005 - 15:53:01 PDT
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