Simulated annealing out of mainstream

From: Francesco Pietra (
Date: Sat Jul 21 2007 - 08:18:25 CDT

I have looked at tutorials and the mailing list. I am a little out of the
mainstream, desiring to find the absolute minimum for non polymeric large
molecules (50-600 atoms) under a variety of conditions, final aim being the
interaction with receptors.

To start with, I would appreciate having suggestions as to suitable scripts

1)Simulated annealing in vacuum, where the barriers to certain dihedral
inversion are rather large, ca 25 kcal/mol.

2) Do the same in implicit solvent.

3) Do the same in explicit solvent. Solvents range extensively in polarity,
from chloroform to water. Of course I am not aimed in due time at any study of
receptors in chloroform. This solvent is just to have a check against 1H NMR
experimental data, which are most detailed in this solvent.

The conformational energy differences are quite small (as small as 1.5
kcal/mol) and the FF by which I have constructed parameter and coordinate files
is certainly inadequate to such endeavor. Though, what I have hopefully serves
to begin to understand the problems. I used the gaff FF.

Thanks a lot for answering so many questions

francesco pietra

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