[gmx-users] Fatal Equilibration Errors

[Justin A. Lemkul]

Nancy wrote:
> Hello,
> 
> I have successfully minimised and equilibrated one glycerol molecule in 
> a box of water (using the ".mdp" files below).
> 
> I noticed that during both minimisation and equilibration, solvent 
> molecules (waters) form many more hydrogen bonds between each other than 
> the solute (glycerol) forms to the solvent molecules.  Is this normal 
> for such a system?

> nsteps        = 5000
> dt        = 0.002

Basing any conclusions on only 10 ps of data collection is likely insufficient.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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