[gmx-users] Turn off the electrostatic interaction between two particular groups
ljgsq at yahoo.com
Fri Dec 25 05:17:31 CET 2009
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.
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?
Thanks very much!
Merry Christmas and a Happy Holiday!
National University of Singapore
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