AMBER Archive (2006)

Subject: RE: AMBER: density

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed May 17 2006 - 23:11:11 CDT

Hi Mathew,

> Thanks for clarifying my problem. I have just used the
> process_mdout.perl script and plotted the
> summary.DENSITY using xmgrace. In the graph it is
> found that the density is go on increasing.
> Actually I dont want to calculate density. I just want
> to verfy that whether there is any problem with my
> simulation.

This is a function of the way xmgrace works. If you look at the
summary.DENSITY file you will find that it only contains 1 column, in this
case time. No column containing the density data is present since there is
no density information in the output file. Xmgrace when presented with a
file containing only 1 column assumes that is y data and plots this against
entry on the x axis.

What you should look at to check you calculation is a combination of things.
First check that your pressure and density in the constant pressure part of
your simulation actually equilibrated before you switched to constant
volume. Then you should look at Potential and total energy vs time as well
as the temperature. You should also calculate the RMSD to the starting
structure as a function of time and look for any sudden jumps in this etc.

Above all when you seemingly get results you don;t understand it doesn't
hurt to actually look at the raw data that is being plotted and the error
should be obvious.

All the best
Ross

/\
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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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