[gmx-users] Gravity in MD-simulations

[David van der Spoel]

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
> ------------------------------------------------------------------------------
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++