VMD-L Mailing List

From: Peter Freddolino (petefred_at_umich.edu)
Date: Mon Jun 08 2020 - 10:05:07 CDT

Please have a look at the documentation on the namdenergy webpage (
https://www.ks.uiuc.edu/Research/vmd/plugins/namdenergy/). If you set up
periodic boundary conditions, it will allow you to also use PME. Whether or
not you do so depends on the questions that you're asking, and how your
system is set up.
Best,
Peter

On Mon, Jun 8, 2020 at 10:54 AM Francesco Pietra <chiendarret_at_gmail.com>
wrote:

> 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.
>
> francesco
>
> On Sun, Jun 7, 2020 at 5:43 AM Peter Freddolino <petefred_at_umich.edu>
> 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 <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/
>>>
>>>