Hi all,
We have a requirement to run some large simulations using NAMD, and the
system includes a bunch of nonstandard items that are not parameterized
in the force field that comes with NAMD. As a solution, we are
considering using Amber's prmtop and coordinate files.
Now, we see two possible ways to do this: First: minimize and
equilibrate using Amber, and then use the restart file of the
equilibrated system for the production run with NAMD. Second: do the
whole thing in NAMD. We are a bit more comfortable with using Amber part
of the way, mostly due to more experience with it..
The question is: are there any substantial differences between these two
approaches? If the system is minimized and equilibrated in Amber, and
then simulated with NAMD, will it affect the outcome? Can anyone comment
on possible issues?
Thanks in advance for any comments
Sasha
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Received on Wed Mar 04 2009 - 01:26:04 PST
