AMBER Archive (2009)

Subject: Re: [AMBER] A good way to use an Amber force field with NAMD?

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Tue Mar 03 2009 - 18:08:33 CST

Assuming the NAMD implementation of the Amber force field is correct,
I don't see a reason for the two approaches to yield different
results. In fact, if you are going to (have to) trust the NAMD results
for the production run, why not trust them for the equilibration run
as well?

Gustavo.

On Tue, Mar 3, 2009 at 4:37 PM, Sasha Buzko <obuzko_at_ucla.edu> wrote:
> Hi all,
> We have a requirement to run some large simulations using NAMD, and the
> system includes a bunch of nonstandard items that are not parameterized in
> the force field that comes with NAMD. As a solution, we are considering
> using Amber's prmtop and coordinate files.
> Now, we see two possible ways to do this: First: minimize and equilibrate
> using Amber, and then use the restart file of the equilibrated system for
> the production run with NAMD. Second: do the whole thing in NAMD. We are a
> bit more comfortable with using Amber part of the way, mostly due to more
> experience with it..
>
> The question is: are there any substantial differences between these two
> approaches? If the system is minimized and equilibrated in Amber, and then
> simulated with NAMD, will it affect the outcome? Can anyone comment on
> possible issues?
>
> Thanks in advance for any comments
>
> Sasha
>
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