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:
table_whateveryoulike_groupA_groupB.xvg
table_whateveryoulike_groupA_groupC.xvg
table_whateveryoulike_groupB_groupC.xvg
...
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,
M.
--
Massimo Sandal, Ph.D.
http://devicerandom.org
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