AMBER Archive (2005)

Subject: AMBER:

From: Simon Whitehead (SJW084_at_bham.ac.uk)
Date: Thu Jun 02 2005 - 07:44:03 CDT

Some of the minimisations that i carry out end with the error "LNMIN FAILURE" and i am not sure what it means. However the DRMS (in region of 5E-3) and GMAX (in region of 1E-1) values both appear to be decreasing. Further to this I was wondering, is there any sort of consensus regarding a DRMS value that should be aimed for during minmisation prior to performed dynamics runs and what kind of effect does this have on the simulations or is it just mainly to remove any bad contacts? I have experimented with using a solvent shell instead of a periodic box in order to reduce the solvent content of my system however the DRMS value during minimisation does not drop below ~2E-1, is this is due to the solvent shell? Does anyone know if running the a minimmisation step with the solvent constrained would give a better impression of the protein minimisation.
 
Kind Regards
 
Simon Whitehead
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