[gmx-users] Replica exchange
devicerandom at gmail.com
Sat Nov 27 19:48:11 CET 2010
On 27/11/10 17:49, Sai Pooja wrote:
> 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
> (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:
> 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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