[gmx-users] group by atom type in .GRO ?

X.Periole X.Periole at rug.nl
Tue Jul 25 09:32:13 CEST 2006

> Hello I have a system with Lipids, gold and solvent. I 
>generate the
> .gro file myself with a script. Should I group the 
>molecules together,
> ie the lipids first then the gold and the solvent after, 
>or can they
> be all mixed up?
> The errors I get right now is the following:
> Warning: atom names in topol.top and conf.gro don't 
>match (Au - HS1)
> (and there is many of them)
> I am sure my .itp file works because I have tested it 
> with simple systems...

It is always better to have things in order .. but it is
not required. I would advice to put lipid/solvent/gold
together for analysis purpose.
The only thing you have you have to make sure is that
the order of the molecules are the same in the gro file
and in topol.top: that is what the error message is about 

> Moreover I wanted to ask also what is better to make an 
> minimization by blocking a group of the atoms. Should I 
>use a freeze
> group or position restraints ? I should add that I don't 
>really care
> if the atoms move around a little.

position restrains give more fredom to the system to
minimize. If you don't have specific reason to fix atoms
let them free ...


More information about the gromacs.org_gmx-users mailing list