[gmx-users] Turn off the electrastatic interaction between 2 energy groups
xhuang at chem.columbia.edu
Wed Feb 11 19:08:01 CET 2004
Thanks for your reply, maybe I did not explain clearly.
What I mean of turning off the electrastatic interaction between 2 energy
not only substracting the energies but also not computing the forces due to
interaction when you update the forces and the velocities in MD silmulation.
----- Original Message -----
From: "Uwe Richter" <quantix1 at gmx.de>
To: <gmx-users at gromacs.org>
Sent: Wednesday, February 11, 2004 12:25 PM
Subject: Re: [gmx-users] Turn off the electrastatic interaction between 2
> it's not totally clear to me what you want to do but you could subtract
> electrostatic interactions between the two groups afterwards. If the
> energy groups are defined properly the information is written in the
> edr file, the final interaction energies also in the log file.
> > Hi all,
> > I already posted this question on the developer's list, but nobody
> > answers it. So I posted it here again.
> > Inomacs, "energygrp_excl" can exclude all non-bonded
> > interactions between pairs of energy groups. But I only want to
> > turn off the electrastatic interaction between 2 energy groups.
> > The following is my idea. (I choose Cut-off for electrastatic
> > calculation and use grid for the neighbour searching.)
> > There are 3 short range neighbour-lists generated in ns.c(vdw,
> > coup, vdwc). It seems to me that "vdwc" will store the information of
> > the
> > particls with both charges and the lj type. "vdw" will store the
> > information of the particles whose charge is 0, and "coup" will store
> > the information
> > of the particles whose lj is 0.(not sure?) What I have done is to loop
> > over the charge groups and judge if the 2 groups are excluded, if they
> > are,
> > I just add the particles in that group into "vdw" list instead of "vdwc"
> > list. Then it seems to me that only vdw interaction is computed even if
> > the
> > charge are not 0 for those particles.
> > But when I tested it, it did not work. Before I did the exclusion,
> > the elecstatic intereaction of the system is 0.16 kj/mol, but after I
> > chose the
> > exclusion, the elecstatic intereaction of the system is -201 kj/mol. It
> > seems that the 1-2, 1-3 neigbours are even computed. (My system includes
> > 1 spc water molecule and 1 pf6 molecule).
> > Do you know what is wrong with my idea, and is there a better way
> > to do this?
> > Thank you very much!
> > Best
> > Xuhui
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