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