[gmx-users] Post-analysis of residue residue interactions

CROUZY Serge 119222 serge.crouzy at cea.fr
Thu Feb 2 14:40:53 CET 2017

Dear gromacs users

We've run umbrella sampling simulations (with pull) of proteinA/ProteinB dimer turning into two separate monomers
We have 25 simulation windows each of 10 ns MD (1000 frames) and proteins containing 132 residues
We now want to calculate interaction energy (VDW Elec) between each residu of B (1 by 1) and all residues of A (as a whole) to understand which residues most contribute to the PMF

 The way we do that is described below : 
for (( f=0; f<=25; f++ ))                                (all frames)
for (( res =1; res<=132; res++ ))                 (all residues) 
make_ndx  ResInter                                 define residue number in B : Resinter
gmx_mpi grompp                                 build tpr  define new energy groups energygrps  =  A ResInter
mpirun -np 8 gmx_mpi mdrun -rerun umbrella$f.xtc                   rerun dynamics on the 1000 frames 
g_energy                                                    average energy between Resinter and total A protein 

that's 25*132*1000 = 33 10⁵ energy calculations and particularly time consuming 132*25 = 3300 times rereading
the trajectories 

I was wondering is there a more efficient way to do this ? For instance reading each trajectory only once instead of 132 times
That's basically exchanging loop order
for (( f=0; f<=25; f++ ))   (all frames)
   mpirun -np 8 gmx_mpi mdrun -rerun umbrella$f.xtc 
   for (( res =1; res<=132; res++ ))
but this does not seem possible because the interacting groups have to be defined before calling md rerun

Any idea would be greatly appreciated


Serge Crouzy

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