[gmx-users] Looking for the source of the H-REMD slowdown when decoupling a lot of atoms

[Michael Shirts]

Hi, Chris: I'm pretty sure that it's because the nonbonded free
energies are much slower than the standard free energies.  You state:

> I took a look at gmxlib/nonbonded/nb_free_energy.c in v.5.1.2, but I was unable to find a function called "gmx_waste_time_here()" and beyond that I was out of my depth.

But it's much more the fact that the non-free energy nonbondeds are
SUPER optimized.

I don't see a particularly viable way around this for now. The only
thing I can think of splitting the neighborlists into two force calls,
and scaling the forces and energies coming out of those.  That would
be a huge pain.

On Tue, Mar 29, 2016 at 9:50 PM, Christopher Neale
<chris.neale at alum.utoronto.ca> wrote:
> Dear Users:
>
> I am trying to do some Hamiltonian replica exchange (H-REMD) in gromacs 5.1.2 and am running up against really large slowdowns when decoupling a large number of atoms. I am decoupling 5360 atoms out of the 15520 atoms in my system. The goal is not to get a PMF, but to enhance sampling using the REST approach to partially decouple lipids in a bilayer. This approach enhances lipid relaxation times ( http://pubs.acs.org/doi/pdf/10.1021/ct500305u ) though the authors of that paper modified the gromacs code to do their own H-REMD in order to avoid the really slow speed they also got when decoupling lots of atoms via the free energy code.
>
> I have already posted details here http://redmine.gromacs.org/issues/742 , which includes .mdp options and some timing output. I compare the timing output to a standard temperature REMD (T-REMD) run. For my usage, the slowdown is about 12x for H-REMD vs. T-REMD.
>
> I am motivated to find a solution within gromacs because the alternative is to use gromacs 4.6.7 with plumed (or with the aforementioned modified code, which is also gromacs v4). Normally that would be a viable option, but I am using the charmm force field and the charmm TIP3P water and I would rather not give up the speed boost that I see in gromacs v5.1.2, which allows the use of the verlet cutoff scheme and has been tested and shown to give the correct reproduction of charmm forces (vs. the forces one would get using the charmm simulation software).
>
> I took a look at gmxlib/nonbonded/nb_free_energy.c in v.5.1.2, but I was unable to find a function called "gmx_waste_time_here()" and beyond that I was out of my depth.
>
> Thank you for any pointers,
> Chris.
>
>
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