[gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3

[Harry Saavedra]

Hi,
My system is composed of 900 copies of the same small molecule without charges (atoms a1, a2, a3 + a virtual site). All the atoms a1..a3 interact using a tabulated potential 1 and all the virtual sites of every molecule interact using tabulated potential 2. (The system has two energy groups). This is the reason why I wanted to use two energy groups in the test particle.

For curiosity, does Gromacs use the Cavity Insertion Widom method?

Thanks for the advice !

Harry G.

From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3
Date: Fri, 15 May 2009 09:18:56 +0200








Hi,

The issue is slightly different here.
Currently TPI in Gromacs is limited to inserting a single charge group.
Since energy groups should consist of whole charge groups, the inserted
molecule can only consist of a single energy group.
You can solve your problem by making the whole inserted molecule an energy group C
and then define the proper tables between A-C and B-C.

I have no clue how your system looks like, but if you have multiple charge groups,
won't you molecule be to large for use with TPI?
TPI will only work for molecules that are small enough to fit into spontaneously
occurring cavities.

Berk

> Date: Fri, 15 May 2009 07:50:52 +1000
> From: Mark.Abraham at anu.edu.au
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3
> 
> Harry Saavedra wrote:
> > Dear All,
> > 
> > I run a test molecule insertion simulation using Gromacs 4.0.3. All the 
> > molecules of the system work with two energy groups (two tabulated 
> > potentials), and every atom belongs to a different charge group; but 
> > Gromacs shows an error message:
> > 
> >  > grompp...
> >  > mdrun ...
> > 
> > Program mdrun, VERSION 4.0.3
> > Source code file: force.c, line: 1068 Send <javascript:;>
> > Fatal error:
> > The molecule to insert can not consist of multiple charge groups.
> > Make it a single charge group.
> > 
> > 
> > However,when I set all the atoms of the inserted molecule (A,B,C..) to 
> > the same charge group (cgnr in the top file), Gromacs displays :
> > 
> > 
> >  >grompp...
> > 
> > Program grompp, VERSION 4.0.3
> > Source code file: grompp.c, line: 150
> > Fatal error:
> > atoms A and B in charge group Z of molecule type 'Protein' are in 
> > different energy groups
> > 
> > 
> > There is any way to overcome this problem? How Gromacs can ignore the 
> > charge groups?
> 
> Energy groups are set in the .mdp file using the groups defined 
> (implicitly) in the .ndx file. You need a charge group that is a subset 
> of a single energy group.
> 
> Mark
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