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
--
========================================
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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