On Tue, May 28, 2013 at 10:33 AM, Francesco Pietra <chiendarret.gmail.com>wrote:
> Hi Daniel:
>
> The title indicates that I was running AMBER FF. Perhaps I should have
> specified 99SB. I was simply asking whether the flags I used for TIP3 water
> are correct when using NAMD-CUDA as engine. I wanted to freeze water O-H
> bonds only. As the simulation proved slow, I was wondering whether my aim
> was accomplished by the flags used.
>
> I have my reasons to use that engine and AMBER FF. The first, because, once
> the system is equilibrated, I want to run a particular biased MD that is
> not available with the AMBER engine, either sander or pmemd. The second,
> because transition metal prosthetic groups, as in my protein, can be rather
> smoothly parameterized under 99SB.
>
I think Dan's main point was that the typical users on this list are well
versed in using the Amber programs (sander, pmemd), but are maybe not as
experienced with NAMD. It is more likely that NAMD users have seen and
fixed this error than Amber users.
Therefore, cross-posting on the NAMD mailing list is more likely to get you
a fast, helpful response than just posting here.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue May 28 2013 - 08:00:04 PDT
