[gmx-users] Test Particle Insertion Problem-Gromacs 4.0.3
gmx3 at hotmail.com
Fri May 15 09:18:56 CEST 2009
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
> 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
> > 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.
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
What can you do with the new Windows Live? Find out
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users