[gmx-users] Can Gromacs 5.0~5.1.x perform Implicit solvent simulation

Mark Abraham mark.j.abraham at gmail.com
Tue Dec 29 14:51:42 CET 2015


Implicit solvent support hasn't been actively maintained since GROMACS 4.5.
If 4.5 running on a multi-core x86 is too slow, then you should explore
other programs, e.g. AMBER


On Tue, Dec 29, 2015 at 2:01 PM Chunlei ZHANG <chunleizhang.pku at gmail.com>

> Dear Gromacs developers and other users,
> I would like to simulate a protein complex of 0.5 million atoms by using
> implicit solvent model (i.e. GB model).
> I has successfully simulated the system with Gromacs 4.5.1 by using
> particle decomposition. But it is quite slow.
> Since versions > 5.0 support GPU, I want to take advantage of this feature,
> but find mdrun does not support particle decomposition.
> Does anyone know how to use Gromacs >5 together with GB model?
> Thanks in advance.
> Chunlei
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