From: Francesco Pietra (
Date: Mon Jun 08 2020 - 09:53:58 CDT

As far as I can see from the namdenergy-generated namd config file, namd is
run under implicit solvent conditions (some sort of MM_GBSA?). Although the
submitted system is heavily water solvated.

I tried namdenergy with a RNA-small organic molecule complex and values for
pi-pi and halogen-pi stacking are found in a reasonable range.


On Sun, Jun 7, 2020 at 5:43 AM Peter Freddolino <> wrote:

> 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 <> 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
>> 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
>> Phone: 217-244-3349