On Mon, Aug 8, 2011 at 5:19 PM, Ismail, Mohd F. <farid.ou.edu> wrote:
> Hi,
>
> I want to simulate bulk small organic molecules, and using GAFF and sqm I
> created the topology for a test system (dimethoxy ethane). Lets say after
> running constant pressure simulation, the density doesn't converge to the
> experimental value, could the problem be the partial charges, or is it the
> force constants?
>
Unless the geometries for your small organic molecules are significantly
warped to the point where it inhibits normal packing (which is probably
unlikely), it's almost certainly the nonbonded parameters that are causing
your issues (that is, either the partial charges or the VDW interactions).
> Another question I have is, is there a certain cutoff that I should use for
> vdw? I know usually it is between 8 to 12, but is there a rule of some sort
> to choose this? If the parametrization use a particular cutoff, is it safe
> to change the cutoff for my molecule?
>
There's no hard-and-fast rule for this. As I understand, the VDW cutoff for
PME calculations is typically the same as the direct space cutoff (at least
for Amber that's true, I think). I don't think it's unsafe to increase the
cutoff as much as you'd like, since I expect the VDW contributions decay too
quickly to have much contribution past 8 to 12 Å (I would be wary of
decreasing it, since, at the very least, you won't be conserving energy very
well).
HTH,
Jason
>
> Farid Ismail
> Graduate Student
> Dept. of Chemistry/Biochemistry
> University of Oklahoma
>
>
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Aug 08 2011 - 19:00:02 PDT
