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

[Mark Abraham]

Hi,

Great. (Of course, prove the concept with energygrps = A ResInter1
ResInter2 manually before evolving the script)

Mark

On Fri, Feb 3, 2017 at 2:32 PM CROUZY Serge 119222 <serge.crouzy at cea.fr>
wrote:

> Yes that's a good idea
> I didn't know about different energy groups
> I'll try that
> Thanks a lot Mark
>
>
> -----Message d'origine-----
> De : gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> gromacs.org_gmx-users-bounces at maillist.sys.kth.se] De la part de Mark
> Abraham
> Envoyé : vendredi 3 février 2017 14:19
> À : gmx-users at gromacs.org
> Objet : Re: [gmx-users] Post-analysis of residue residue interactions
>
> 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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