AMBER Archive (2005)

Subject: RE: AMBER:

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jun 03 2005 - 11:51:48 CDT

> Some of the minimisations that i carry out end with the error
> "LNMIN FAILURE" and i am not sure what it means.

See http://amber.scripps.edu/Questions/linmin.html

> However the
> DRMS (in region of 5E-3) and GMAX (in region of 1E-1) values

This is pretty damn good, especially if you just want to do MD on the
structure.

Typically before starting MD you only need to do a few hundred steps or so
of minimisation to clean up the structure. See the tutorials for examples:
http://amber.scripps.edu/tutorial/index.html

> have on the simulations or is it just mainly to remove any
> bad contacts?

It is purely to remove bad contacts and stop your system blowing up because
hydrogens were placed in non-optimal positions. When you run the MD you will
be equilibrating the system so it quickly move out of the minima the
minimisation was heading towards.

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 |
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