From: Alexander Predeus (predeus_at_gmail.com)
Date: Tue Oct 19 2010 - 18:20:12 CDT
Dear all,
I wanted to ask for your input on two loosely related matters related
to molecular dynamics in explicit solvent. It seems that a lot of NAMD
users simulate large systems with explicit solvent, so it has to be a
good place to ask :)
First, it seems like there are not that many parameters in NAMD that
allow you to manipulate PME, like the width of Gaussian distribution,
order of spline interpolation etc. Was that found to be not that
important?
Second, I noticed that NAMD uses default cuton of 8.5A and cutoff of
10A (at least with CHARMM27 force field). How many users actually use
defaults? I understand that larger cutoff will make simulation slower,
but I also came across the information that switching van der Waals
forces earlier than 12A can significantly influence the vdw packing of
proteins, and now I'm concerned about how big could this influence be.
Thanks in advance!
- Alex Predeus
Michigan State Universtity
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