[gmx-users] GPU Acceleration in case of Implicit Solvent Simulations

Mark Abraham mark.j.abraham at gmail.com
Fri Aug 29 11:17:19 CEST 2014

On Thu, Aug 28, 2014 at 11:59 PM, Siva Dasetty <sdasett at g.clemson.edu>

> Dear all,
> Can we use periodic boundary conditions in case of implicit solvent
> simulations?

Yes (but I only recommend doing so in GROMACS 4.5.x)

> If so, why?

In general, why not? It's a boundary condition. What's special about
infinite boundary conditions?

> Also, can implicit solvent model in gromacs in any version (till 5.0) be
> implemented in more than 2 processors or can it at least use GPU
> acceleration provided by gromacs?

No - the implicit solvent code has been unmaintained in practice, starting
with 4.6. Last I looked, only infinite boundary conditions and a single
thread worked. You'll probably get better mileage on GPUs with AMBER, which
actively targets this type of simulation.

I have tried using pbc=no and group cut-off scheme in gpu based gromacs
> V5.0, but there is a warning which says GPU is disabled because it
> effectively works only with verlet cut-off scheme and verlet cut-off scheme
> requires pbc=xyz or xy.

Correct. In 4.6 and 5.0, the required machinery for using GPUs and doing
implicit solvation are almost completely mismatched.


> Also tried implementing in gromacs version 4.5.5 using openMM after
> following the installation instructions in the following link, (
> http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GROMACS-OpenMM
> )
> and here again there is no luck as we dont have the compatible hardware.
> Thanks,
> Siva
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