GROMACS version: 4.5.5
GROMACS modification: No
Hi,
I’m trying to run a protein-water system where the beads interact by a special vdW potential. To apply this special potential, I prepared several tabulated potential files such as table_A_A.xvg, table_A_B.xvg, table_A_C.xvg … (including all possible vdW pairs). In the .mdp file, I also defined energygrps = A B C …(including all kinds of bead) and energygrp-table = A A A B A C… (corresponding with tabulated potential files).
While executing mdrun, I am using the follwoing command ‘mdrun -deffnm md -table table.xvg’. Then Gromacs begin to read all tabulated potential files as mentioned in .mdp files and choose the right tabulated potential file when discribing the corresponding vdW interactions (for interactions between A and B, using table_A_B.xvg, etc). These all work very well.
However, when I try to introduce pair interactions in my system, I failed to define different kinds of pair interactions using ‘-tablep’ option. First, I added many kinds of pair interactions in .itp file (in [pairs] section). Then I prepared tabulated pair potential files tablep_A_B.xvg, tablep_C_D.xvg… (corresponding with pair definitions in .itp files). After that, I executing mdrun using ‘mdrun -deffnm md -table table.xvg -tablep tablep.xvg’ hoping that Gromacs can read all kinds of pair potential files mentioned above and choose different tablep_X_Y.xvg when discribing the corresponding pairs like how ‘- table’ works. But the program remind me to provide tablep.xvg. After I test many times, it seems that all the pair interactions are defined by one single file, that is tablep.xvg (the file before ‘-tablep’ option), which means different tablep_X_Y.xvg I provided are useless.
I wonder if there are some ways to correctly use ‘-tablep’ option in mdrun so that I can freely define different kinds of pair interactions and use various tabulated pair potential files like the way we used in ‘-table’ option. I would be very appreciate if you could give me some advice!
Thanks for your time!