[gmx-users] regarding table for water water interactions

Mark Abraham mark.abraham at anu.edu.au
Wed May 25 11:51:49 CEST 2011

On 25/05/11, sreelakshmi ramesh  <sree.lakshmi at research.iiit.ac.in> wrote:
> Hai all,
>           My system is just a water Spc model. 
>           I am trying to create a table.xvg which would deal with nonbonded intearction for water-water for say SPC model.
> If i have to calculate the potential i have to consider the  interaction between 
> 1.O of water1--O of water 2(LJ+COLOUMB)  [CREATED A TABLE that containsr, f (r), −f (r), g(r),−g (r), h(r) and −h (r)  ]
> 2.H of water 1--O of water 2(COLOUMB)        [ are tables needed ?]
> 3.H of water 1--H of water 2(COLOUMB)         [are tables needed ?]

That depends whether you're trying to apply a different or the same functional form to the interactions of the hydrogen atoms, i.e. whether you have an energy group for the whole system, or have O and H in different energy groups so that you can apply different functional forms to different interactions.

> for 2 and 3rd case should i create 2 tables respectively ? if not how is the potential is calculated  for the the last two cases ?

The user table applies to all interactions unless you start playing around with energygrp_table. So your hydrogen interactions use the table, but only look up the values for f.

> and if it has to be to created since the lennard jones part say g(r),−g (r), h(r) and −h (r) is zero for all values of r should i just create a table with r,f(r)and -f'(r) for last two cases?

6.7.2 covers this last point.


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