i guess it's also the case for the TIP5P, regarding the ions
parametrization, right?
I was already planning to investigate the water alone. And thanks for
the tip about the time step. I thought that 1fs would be enough.
On 7/21/11, David A Case <case.biomaps.rutgers.edu> wrote:
> 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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--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Thu Jul 21 2011 - 07:00:03 PDT
