Speeding up: Dummy constructions for aromatics or hydrogens

From: DimitryASuplatov (genesup_at_gmail.com)
Date: Fri Apr 17 2009 - 12:11:27 CDT


I`ve been using gromacs previously. It is generaly a default strategy in
gmx to use dummy constructions for hydrogens or aromatics and heavy
hydrogens constructions. This enables fast and reliable calculations
with up to 4fs.

1/ Is it possible to set dummy constructions in namd? How? I did not
find anything appropriate in the manual or on the web

2/ What are the general strategies to speed up the calculations in namd?

Thanks, I appreciate your time.

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