[gmx-users] Re: Error in Membrane simulations with POPC bilayer
jalemkul at vt.edu
Tue Jul 17 12:47:49 CEST 2012
On 7/17/12 4:05 AM, J Peterson wrote:
> Hi Justin,
> I have the following Notes during NPT equilibration.
> NOTE 1 [file pr_NPT.mdp]:
> nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
> nstcomm to nstcalcenergy
nstcalcenergy tries to improve performance by reducing global communication. If
you set nstcomm to a more frequent interval of steps, you're doing global
communication more frequently, hence making nstcalcenergy relatively pointless,
so grompp sets them both to nstcalcenergy for efficiency.
> NOTE 2 [file pr_NPT.mdp]:
> leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
As stated in the manual, NH chains > 1 can only be used with a velocity verlet
> What do they really mean? Is the system safe with these notes?
Yes. These are normal messages.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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