From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Aug 04 2016 - 17:21:40 CDT
Based on your description, and for the reasons Brian mentioned, NAMD is
probably not the right software for your project.
On 4 August 2016 at 22:17, Brian Radak <bradak_at_anl.gov> wrote:
> 1.) I'm not sure you can turn off the computation of electrostatics
> completely, but using "PME off" should bypass a lot of the computational
> cost. You can turn off the effect of electrostatics in a number of ways,
> for example by zeroing the charges or just using "nonbondedscaling 0", but
> the latter also turns of LJ interactions I believe.
> 2.) TclForces is a good sandbox for trying new models, but I wouldn't
> necessarily recommend it for production runs of something like brute force
> protein folding.
> If you are doing pairwise potentials, you can also try using the tabulated
> non-bonded interactions, but these might not be well-typed for what you
> Unfortunately (fortunately?) the main purpose of NAMD is exactly to
> accelerate the electrostatics, so those routines are a pretty essential and
> central part of normal execution. You'd have to tell use more about what
> kinds of models you want to use to get more specific advice.
> On 08/04/2016 01:15 PM, Emerson Macedo wrote:
>> Hello NAMD experts!!
>> I am new with NAMD and currently working on
>> adapt it to our research with proteing folding simulations.
>> My current challenge involves the possibility of using our
>> implementation of electrostatic force calculations instead of NAMD's
>> My first thought was (naive I guess) find a way to
>> disable NAMD version and then add out implementation.
>> Here my questions:
>> 1) How does one could disable NAMD electrostatic calculations or replace
>> 2) Does it make sense to use TCLForces API to implement our version or
>> would be
>> better to implement directly in the source code?
>> Any directions would be very much appreciated.
>> Thank you all for any help.
>> My best regards,
> Brian Radak
> Postdoctoral Appointee
> Leadership Computing Facility
> Argonne National Laboratory
> 9700 South Cass Avenue, Bldg. 240
> Argonne, IL 60439-4854
> (630) 252-8643
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