Thank you Jason. I will try RED to get my charges. I've tried a few different cutoff and it is still a little higher (~.900 instead of .868) than the experimental value. The geometries look fine as far as I can tell.
I see some of the benchmark mdin files have the cutoff as high as 16. I think I will try that too.
Best regard,
Farid Ismail
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Monday, August 08, 2011 8:34 PM
To: AMBER Mailing List
Subject: Re: [AMBER] GAFF, Charges, and Cutoff
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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> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Aug 09 2011 - 08:00:05 PDT
