[gmx-users] Replica exchange

ms devicerandom at gmail.com
Sat Nov 27 19:48:11 CET 2010

On 27/11/10 17:49, Sai Pooja wrote:
> Hi,
> I am running a script that uses mdrun of gromacs and does replica exchange
> (not using -replex). The reason is that I want to use different table files
> for different replicas. However, it seems that I cannot supply unique table
> names. For example, if I supply a table name different from
> table_Protein_SOL.xvg for protein solvent interactions, like
> rex0_table_Protein_SOL.xvg, I get an error -
> Fatal error:
> Library file in current dir nor  not found table_Protein_SOL.xvgin default
> directories.
> (You can set the directories to search with the GMXLIB path variable)
> For more information and tips for troubleshooting, please check the GROMACS
> To oversome this limitation, I am using something like this:
> [pseudocode]
> for r 1 to n:
>     copy rex_r_Protein_SOL.xvg table_Protein_SOL.xvg
>     mdrun -s .. -table table.xvg -table table_Protein_SOL.xvg ...
> Will mdrun be able to run with separate table parameters in this way?

I can use different tables with names in a fashion like:

(where GroupA and GroupB can be whatever you want)

Then the mdrun line is
mdrun ...  -table table_B_30_70_0.4.xvg

and then mdrun takes care of looking after the GroupA_GroupB , 
GroupB_GroupC etc. tables, depending on your .mdp file.

Hope it helps,

Massimo Sandal, Ph.D.

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