From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Jun 08 2020 - 11:00:54 CDT

My bad.
Under periodiboundary/pme was slower, but not so much

thanks a lot
francesco

On Mon, Jun 8, 2020 at 5:03 PM Peter Freddolino <petefred_at_umich.edu> wrote:

> 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/
>>>>
>>>>