[gmx-users] leapfrog does not yet support Nose-Hoover chains

Mark Abraham mark.j.abraham at gmail.com
Mon Feb 3 18:38:01 CET 2014


Protein chains and NH chains are entirely different things (see manual for
latter). Probably for ligand-protein simulations the difference between NH
with 1 chain and more is marginal, and probably smaller than your sampling
error. You could a) use md-vv to get NH chains (but slower when run in
parallel), b) use v-rescale thermostat, c) change nothing and hope for the


On Mon, Feb 3, 2014 at 4:28 PM, Mahboobeh Eslami <mahboobeh.eslami at yahoo.com
> wrote:

> hi GMX users
> if i use Nose-Hoover thermostat for ligand-protein simulation, i will get
> following note:
> "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to
> 1."
> my protein has 1 chain.
> is the note important for ligand-protein simulation?
> thanks
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