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

[Berk Hess]

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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