[gmx-users] Having WCA bonded interaction with FENE potential

Mark Abraham mark.j.abraham at gmail.com
Tue Jan 24 16:24:16 CET 2017


Sounds like one approach might be to use FENE bonds, normal exclusions = 3
(or whatever), and to add [ pairs ] function type 1 for each bonded
interaction, and thereby implement your WCA. But these approaches might
differ in how VDW interactions between atoms separated by more than one
bond are computed, and I'm not sure from your description what you intend.
So choose carefully.


On Tue, Jan 24, 2017 at 3:40 PM ARNAB MUKHERJEE <arnabmukherjee249 at gmail.com>

> Hello,
> I am simulating a charged bead-spring modelled polyelectrolyte with FENE
> bond stretching potential and Deby Huckel potential for electrostatics. I
> need to combine FENE bonded interaction combined with WCA potential,
> otherwise the beads overlap with each other since there is no replusive
> term. Before this I ran the same system with no electrostatics, so to take
> into account WCA for bonded interaction I did No. of bonded exclusions
> nexcl = 0, and the results of the simulation seem to be ok.
> Now for the same system with electrostatics, if I do nexcl = 0, then there
> will also be electrostatic repulsion between the bonded beads, which I do
> not want. So, how can I have WCA interaction between the bonded atoms,
> without having electrostatic interaction between them?
> I know in worst case, I can build a table for the bond stretching
> potential, where I can add the WCA term with FENE potential. But is there
> an easier way to do this? As FENE potential is already there as one of the
> bonded interactions in gromacs.
> Thanks a lot,
> Regards,
> Arnab Mukherjee
> --
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list