VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Sat Jun 06 2020 - 22:21:32 CDT

Just a quick note that can make this even easier - if you run namdenergy
with the debug flag set, you can look directly at the namd config file and
inputs that are generated to do the calculation (and even edit them, if
needed).
Best,
Peter

On Sat, Jun 6, 2020 at 3:30 AM John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> NAMDEnergy is s simple wrapper that launches NAMD to perform
> the required calculations. If you're wondering how this is
> done in NAMD, the NAMD User's Guide would be the best reference.
> If you need to know the exact inputs NAMDEnergy sends NAMD, I
> would suggest just reading its source code, it is a fairly
> simple script as I recall. NAMD is doing all of the real work.
>
> Best regards,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Jun 01, 2020 at 05:00:56PM +0530, Aashish Bhatt wrote:
> > Dear Sir
> > I am using NAMD energy plugin to calculate Binding energy.
> > can I get some references for this calculation?
> > BestĀ Regards
> > Aashish
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>
>