Janne Hirvi wrote:
Hello gmx-users!
I would like to inquire if there is some sensible way to take into account
gravity in molecular dynamics simulations. I have understood that it is
possible to introduce constant acceleration on certain group in Gromacs with
options acc_grps and accelerate which the latter should be 0.0 0.0 -9.81E-15
(nm/ps^2) in case of gravity. However if the displacement is proportional to
the second power of time, (x=1/2*a*t^2) simulation of nanosecond should induce
displacement of only 5E-18m, which is neglible. Have I understood this
correctly and/or is there some other way to visualize real gravity effects
within the time-scale of MD-simulations?
Thanks for any help,
Janne
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Janne Hirvi, MSc(Physical Chemistry), Researcher
University of Joensuu, Department of Chemistry, P.O.Box 111 80101 Joensuu, FI
Tel: +358 13 2514544 & +358 50 3474223
E-mail: [EMAIL PROTECTED] & [EMAIL PROTECTED]
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Check:
Nanohydrodynamics simulations: An atomistic view of the Rayleigh–Taylor
instability, by
Kai Kadau*†, Timothy C. Germann‡, Nicolas G. Hadjiconstantinou§, Peter
S. Lomdahl*, Guy Dimonte‡, Brad Lee Holian*,
and Berni J. Alder¶
PNAS April 20, 2004 vol. 101 no. 16 5851–5855
They multiply gravity by some orders of magnitude.
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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