[gmx-users] Temperature coupling groups

Pedro Alexandre Lapido Loureiro paloureiro at biof.ufrj.br
Thu Oct 23 16:22:01 CEST 2003

> Currently I do simulations with the following temperature coupling groups:
> tcoupl                   = Berendsen
> tc-grps                  = POPC Protein SOL Cl
> tau-t                    = 0.1 0.1 0.1 0.1
> ref-t                    = 300 300 300 300
> How can I treat solvent (SOL) and Chloride (Cl) as one group and couple them 
> together to the 300K heatbath ? Simply removing Cl gives an error message.

Make an index group (SOL+Cl) using make_ndx.
Then, you will have three groups (POPC Protein SOL+Cl) in .mdp file.
Don`f forget to use -n file.ndx flag when running grompp.


Pedro Alexandre Lapido Loureiro
Laboratório de Física Biológica
Instituto de Biofísica

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