[gmx-users] g_mmpbsa parameter verify: using last 5ns of MD trajectory for binding energy calculation.

[Seketoulie Keretsu]

Dear Expert,

Kindly apologise for putting up a question not exactly related to gromacs.

I have a 30ns protein ligand simulation trajectory from Gromacs. I
would like to use the last 5ns (i.e 25-30 ns) of the trajectory for
binding energy calculation. As mentioned in the g_mmpbasa article i
want to use 10ps snapshots. I assumed that the starting and ending
frames and the 10ps snapshots conditions are passed in the option when
calling the g_mmpbsa command. Kindly verify if I'm doing it right.

g_mmpbsa -f 1EBZ.xtc -s 1EBZ.tpr -n 1EBZ.ndx -i ../pbsa.mdp -pdie 2
-pbsa -decomp -b 25000 -e 30000 -dt 10

here, -b 25000 is used to indicate that frame at 25ns is used as
starting frame. Similarly -e 30000 is used to indicate ending frame
corresponding to 30ns. Also -dt 10 is use assuming 10ps snapshots will
be used.

Please correct me if I'm wrong. Any references will be appreciated.

Thanks,

Seke