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

[Mark Abraham]

Hi,

You can have more than one energy-group pair-of-interest per rerun. That
will compute more pairwise combinations that are not of interest, requiring
more sophisticated use of gmx energy, but this will run a lot faster than
the I/O you're saving. e.g.

energygrps = A ResInter1 ResInter2 ... ResInterN for some chunk size of N
distinct residues of B.

IIRC there's a cap of 64 energy groups because of how they were used in the
implementation of the old group scheme.

Mark

On Thu, Feb 2, 2017 at 2:41 PM CROUZY Serge 119222 <serge.crouzy at cea.fr>
wrote:

>
> 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$f.xtc                   rerun
> dynamics on the 1000 frames
> g_energy                                                    average energy
> between Resinter and total A protein
> done
> done
>
> that's 25*132*1000 = 33 10⁵ energy calculations and particularly time
> consuming 132*25 = 3300 times rereading
> the trajectories
>
> I was wondering is there a more efficient way to do this ? For instance
> reading each trajectory only once instead of 132 times
> That's basically exchanging loop order
> for (( f=0; f<=25; f++ ))   (all frames)
>    mpirun -np 8 gmx_mpi mdrun -rerun umbrella$f.xtc
>    for (( res =1; res<=132; res++ ))
>      g_energy
>    done
> done
> but this does not seem possible because the interacting groups have to be
> defined before calling md rerun
>
> Any idea would be greatly appreciated
>
> Thanx
>
> Serge Crouzy
>
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