AMBER Archive (2006)

Subject: RE: AMBER: question about QM/MM in amber9

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu May 25 2006 - 10:33:17 CDT

Hi Aixiao

> I have a question about the QM/MM module in Amber9, I
> don't know if QM/MM can define the QM center dynamically, did
> not find it in manual. For example, for receptor+ligand
> simulation in Waterbox, first I define ligand and one water
> near to it as QM center, but later, after running MD for tens
> or hundreds ps, this water molecule may go far from the
> ligand and have no interaction with it, while another water
> come to the ligand, so, is it possible to change QM center
> dynamically during MD? Based on distance from ligand or some
> other criteria instead of using residue number?

At present one cannot do this. Computationally it is not simple as there is
a very large amount of bookkeeping involved. This feature may be available
in Amber 10 but that is some ways off. You could try and work around the
problem in two ways, e.g. apply very very weak constraints on the QM water
molecule so that it stays in the vicinity of the QM region. Although this
may affect the overall dynamics. You could also script things to run say
25ps of simulation, have ptraj find you the atom numbers of the closest
water and then use these to write your input file for the 25ps. In this way
you could 'dynamically' alter the QM region in 25 ps steps. If you script it
carefully you should be able to make it entirely automatic. Again not ideal
but these are the only options at present.

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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