[gmx-users] Turn off the electrostatic interaction between two particular groups
Mark.Abraham at anu.edu.au
Fri Dec 25 05:40:37 CET 2009
Li Jianguo wrote:
> Hi all,
> I am wondering if Gromacs allows to turn off the electrostatic
> interaction between two particlular groups. For example, in my
> molecule, there are two charged groups, Grp1 and Grp2. I want to turn
> off only the electrostatic interaction between Grp1 and Grp2. What I am
> thinking is as follows:
> 1) Use the energygrp_excl to turn off both the electrostatic and LJ
> interaciton between Grp1 and Grp2. However, this may lead to serious
> problems as Grp1 and Grp2 can overlap.
Atoms may not belong to more than one group of any type (see manual). So
you will have to construct groups in which you do not want further
> 2) To add LJ interaction between Grp2 and Grp1, I manually introduce an
> artificial group (Grp3) in my toplology file. The parameters and the
> coordinates for Grp3 is the same as Grp 1, but with no charges. So all
> the interactions with Grp3 is only LJ interaciton.
> 3) Then I use energygrps_excl to trun off the interactions between Grp3
> and all the other atoms except the interactions with Grp2. In such a
> case, the LJ interaciton between Grp1 and Grp2 is added.
> I am wondering if the above work. Does Gromacs allow two groups of atoms
> (i.e., Grp1 and Grp3) totally overlap? Or is there any other ways to
> turn off the electrostatic interaction between two particular groups?
There's no simple mechanism to selectively turn off only the
electrostatic nonbonded component. You would either have to zero
parameters in the topology, or do multiple reruns and combine the
results after the fact, or use different user tables for different
groups, depending on your needs.
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