AMBER Archive (2004)

Subject: RE: AMBER: Minimization error

From: Ross Walker (
Date: Wed Aug 25 2004 - 17:35:18 CDT

Dear Armin,

> I checked the first two of your suggestions already.
> No, shake was not turned on.
> Secondly, I went back and ran the tests again. They were fine with 2
> processors, only one that said possible failure. The same was
> true for 1
> processor. The output there was as follows:
> To run it with 1 processor I have to use mpirun -np 1, would
> this make a
> difference somehow?

Only in that you are stil running the MPI version of the code. Just not
actually doing any broadcasts. If the tests all pass ok though then you are
probably ok. It is possible that something is wrong with your system such
that it cannot be minimised well. E.g. if you have two atoms very close
together they will generate a very large initial force. The minimiser will
then take a big step to try and get away from this. It is possible that if
this force is very large you will get radically different behaviour from the
minimiser on different architectures. I would simply try doing some MD with
your minimised structure. If it rapidly blows up (watch it in VMD) then you
most likely have a problem with your molecule.

> I will try your other suggestions soon, I just wanted to know
> the answer
> to these questions sooner.
> As I do not know if the Amber installation on the cluster has
> passed the
> tests, would it make more sense to contact that administrator and ask
> about the tests before performing the short MD runs you suggested?

You could do. It won't take long to run the quick MD runs though and it will
let you know if there is a problem with your molecule. I suspect that what
you have been seeing is an anomally unique to your current initial molecular
configuration and has been fooling us into thinking there is something wrong
with your amber installation. Try out the DNA tutorial simulations and see
if you get similar results for the short MD runs.

Let me know what happens to the MD simulation of your molecule. If the sims
from the DNA tutorial are ok but your molecule blows up then it will confirm
it is a problem with your molecule and not your amber installation. If both
are fine then I give up... ;-)

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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