[gmx-users] Gravity in MD-simulations

David van der Spoel spoel at xray.bmc.uu.se
Tue Aug 29 13:50:49 CEST 2006

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
> ------------------------------------------------------------------------------
> 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: Janne.Hirvi at joensuu.fi & hirvi at cc.joensuu.fi
> ------------------------------------------------------------------------------
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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 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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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