[gmx-users] error after grompp

Abhishek Acharya aacharya at iitk.ac.in
Thu May 9 10:49:28 CEST 2013


> Hi all,
> I need to do simulation which same as protein-ligand tutorial by Justin.
> The different is i'm using my protein and the ligand was zinc.
> I already follow everything in that tutorial and suddenly when i want
> to heat my protein by using the nvt.mdp there was an error state like
> below :
> Fatal error:
> Atom 410 in multiple T-Coupling groups (1 and 2)

This means that atom no. 410 is defined in both the coupling groups which
you have defined in the temperature coupling segment of your mdp file.
Looking at your file it seems to me that the Zn atom is the culprit. In
case the parameters for the Zn are being directly taken from the force
field ions.itp file, then i think gromacs treats this as an ion and would
automatically assigns to Water_and _ions group.
> Actually I do not understand what the error said even when i'm Google
> it to forum there was no one
> facing like mine..Here i put together my topology and the nvt.mdp.
> Hope you can give me some idea that i cant see.
> Another question,why is in the nvt.mdp at the temperature coupling
> there were twice of 300 of tcoupl and also the tau_t : 01. 01. Can u
> explain it why?
this has been explained quite clearly in the gromacs manual. In essence,
defining different coupling groups allows control over the temperature of
the Groups especially protein and water which otherwise have been seen to
differ in the temperature attained by a large degree.


Abhishek Acharya
Structural and Computational Biology Lab
IIt Kanpur

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