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

[Justin Lemkul]

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
>

http://manual.gromacs.org/online/mdp_opt.html#out

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 
integrator.

> What do they really mean? Is the system safe with these notes?
>

Yes.  These are normal messages.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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