VMD-L Mailing List

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Wed Aug 15 2007 - 11:58:41 CDT

And moreover, how should I instruct the plugin to update the selection
every frame?

Cesar Luis Avila escribió:
> Hi Peter,
> thanks for your fast reply. So, it was as i suspected. How should I
> include the solvent in between the molecules on force calculation? It
> is difficult for me to figure it out. Should I include the solvent in
> one of the two selections? for example
> selection1: molecule A
> selection 2: molecule B + solvent slice?
>
> For sure, the number of atoms selected will change from frame to frame
> in this case. I suppose it will introduce an additional problem when
> trying to understand the results.
>
> Thanks again for your help
> Cesar
>
>
> Peter Freddolino escribió:
>> Hi Cesar,
>> this is a good (and important) question. When NAMD calculates pair
>> interactions, it *only* takes into account the atoms which are members
>> of the pair interaction selections, so the forces you obtain from it on
>> the interactions between two sections of solute should be regarded as
>> the forces in vacuum, and interpreted accordingly. You'd have to include
>> some section of solvent in your pair interaction calculations to get its
>> effect included.
>> Best,
>> Peter
>>
>> Cesar Luis Avila wrote:
>>
>>> Dear all,
>>> I want to calculate non bonded forces (VDW and ELECT) between two
>>> groups of molecules during the course of a simulation. For this I plan
>>> to use NAMD energy plugin, with the exact same parameters used for the
>>> simulation (cutoff, pme). This may be a silly question but, when the
>>> electrostatic forces are calculated, does it take into account the
>>> water in between the molecules? In other words, the forces between the
>>> molecules should be regarded as that on vacuum or in a solvated system?
>>> Regards
>>> Cesar
>>>
>>
>>
>
>