[gmx-users] pbc, distance between atoms

[David van der Spoel]

On Fri, 3 Jun 2005, ARGYRIOS KARATRANTOS wrote:

>Hi,
>
>1) Does anyone know with which command I can have pbc in x, y directions but no
>pbc in z directions
you can make the box three times as large (adding vacuum) in the z dir.
>
>2) I am running a polymer with 50 monomer units in water solution. Is it
>possible to measure the distance of 2 atoms of polymer with respect the time of
>the simulation, which command should I use
g_mindist

>Argyris Karatrantos
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-- 
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://xray.bmc.uu.se/~spoel
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