On Thu, Jul 21, 2011, Bruno Rodrigues wrote:
>
> I'm trying to use SPC/F for water to simulate with DNA. However, I could not
> find a parameter file for the ions on this force field.
Joung and Cheatham did not parameterize ion parameters for the SPC/F force
field. As a guess, the spce parameters are probably closest, but I think you
would have to run some salt-water calculations (no DNA) to verify. You should
certainly make sure that you get acceptable results for flexible water (with
or without salt) before adding in DNA, and be aware that you are going into
unexplored territory with this force field combination -- you should expect
surprises and be prepared to experiment. Be sure to use a short enough
time-step -- even 1 fs may be too long for flexible waters.
...good luck....dac
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Received on Thu Jul 21 2011 - 06:00:03 PDT
