AMBER Archive (2005)

Subject: RE: AMBER: minimization stuck problem

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Aug 23 2005 - 10:22:53 CDT

> There is no particular reason why I am not using PME.
> Now I would like to note some things.
> In my 'Case' :) the is strange things. I used PME with cut=10 and
> the EEL from not using PME with CUT=15 are far from each other (
> in the beginning and in the end.) It is like 4 times bigger
> without PME.

This is probably correct, even at 15 angstroms you are still truncating
quite a lot of electrostatic interaction when you don't have PME and so will
get different EEL values and different behaviour in the minimisation. Try
it, run 1 step of minimisation with PME on and try
6,8,9,10,11,12,13,14,15,16 and 18 angstroms. Then try the same without pme
on and plot the total energies in each case as a function of cutoff and you
will immediately see the benefits of PME.

All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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