From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Aug 05 2016 - 02:33:51 CDT
What about the extforces interface?
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Jérôme Hénin
Gesendet: Freitag, 5. August 2016 00:22
An: Namd Mailing List <namd-l_at_ks.uiuc.edu>; Brian Radak <bradak_at_anl.gov>
Cc: Emerson Macedo <emacedo1_at_gmail.com>
Betreff: Re: namd-l: How to replace NAMD Eletrostatic Forces
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 <mailto: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 want.
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 version.
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 them?
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 brian.radak_at_anl.gov <mailto:brian.radak_at_anl.gov>
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