AMBER Archive (2009)

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

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Tue Mar 03 2009 - 18:11:49 CST

Perhaps I can raise a different issue?

I would like a clarification on your statement of: " We have a
requirement to run some large simulations using NAMD". Is this because
you have a contract with them or something ?

Why not use amber (pmemd) directly ? I ask, because the usual comments
about NAMD being much faster or scalable than PMEMD are usually not
quite right.

a.

Gustavo Seabra wrote:
> 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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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry

                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu

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