VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Aug 15 2007 - 20:39:09 CDT

Hi Cesar,
to update every frame, you really ought to use the text interface
instead, and update the selection every frame, eg.

set sela [atomselect top "SEL FOR MOLECULE 1"]
set selb [atomselect top "SEL FOR MOLECULE 2 AND WATER"]

for {set i 0} {$i < LASTFRAME} {incr i} {
    $selb frame $i
    namdenergy -sel $sela $selb ...other args...
}

You can get the options for namdenergy from the manual page or by typing

package require namdenergy
namdenergy

in the tkcon.

Peter

Cesar Luis Avila wrote:
> 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
>>>>
>>>
>>>
>>
>>