[gmx-users] Re: Error in Membrane simulations with POPC bilayer

Justin Lemkul 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.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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