energy group

[Alireza Moradzadeh]

Dear Users,

Let's suppose I have two molecules one composed of three beads and the second one composed of just one bead. mol1 : A B C & mol2 : D

what's is the number of energy groups in gromacs.  should it be like:  mol1 mol2  and energygrp_table: mol1 mol1 mol1 mol2 mol2 mol2 or A A A B A C A D B B B C B D C C C D

Thanks,

Alireza

[Christoph Junghans]

Yes, that is correct!

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> Thanks,
> Alireza
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[Alireza Moradzadeh]

Dear Christoph,

Thank you for your email. But I encountered problem with implementation of it. I want to use PME as my coulomb type. So I have to put my three bead molecule beads in different charge groups. But I face severe problem with electrostatic interaction between beads which blows up my system. I am seeking a way to equilibrate this system.
Thanks
Alireza

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[Christoph Junghans]

2016-02-08 17:40 GMT-07:00 Alireza Moradzadeh <a.m...@gmail.com>:
> Dear Christoph,
>
> Thank you for your email. But I encountered problem with implementation of it. I want to use PME as my coulomb type. So I have to put my three bead molecule beads in different charge groups. But I face severe problem with electrostatic interaction between beads which blows up my system. I am seeking a way to equilibrate this system.

If you need to combine PME with tabulated interactions, you might need
to start from a different initial guess for the potentials, because
the Boltzmann inversion of the g(r) contains contributions from the
coulombic part, too.

I would use a couple of pure LJ interactions for a start (put them as
NAME.pot.in in the same directory as settings.xml).

Christoph

[Alireza Moradzadeh]

In fact, I did the same thing but it worked only for first step then it started to give me LINCS errors. Due to non equilibrated sys.

[Sikandar Mashayak]

Hi Alireza,

Have you excluded interactions between bonded beads? One of your CG molecule has 3 CG beads, so try excluding non-bonded interactions among them and see if that works for you. You can use gromacs [exclusions] setting in your topology to exclude the interactions.

Best,

Sikandar