[gmx-users] Replica exchange

ms devicerandom at gmail.com
Sat Nov 27 19:51:45 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 ...

Since my previous mail was perhaps confusing, I clarify: You should be 
able to use whatever follows the convention:


and you just use

mdrun ... -table table_whateveryoulike.xvg

*without* groupA_groupB ; because then it's mdrun's job (well, grompp 
actually, probably -it's all scripted so I don't remember now!) to look 
after the actual tables' names from the couples defined in the .mdp

Hope it helps,
Massimo Sandal, Ph.D.

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