[gmx-users] simulations of crystal cell possible?

David van der Spoel spoel at xray.bmc.uu.se
Sat Nov 18 09:50:35 CET 2006

Mark Abraham wrote:
>>hello everyone,
>>does anybody know how to simulate crystal cells in gromacs?
>>since the cell size has to be no smaller than twice the cutoff.
>>and if cutoff is too small, the program terminates because of the thus
>>caused too high energy. my cell is very small about 0.7 nm.
> Simulate more than one periodic cell, being careful to construct periodic
> velocities. Perhaps easier said than done, but creating one and
> replicating by hand would be possible - but you'd have to read the source
> code closely.
> Mark
Why would you want periodic velocities? You don't have thos in crystals.
Anyaw genconf will do it without programming.

genconf -nbox 4 4 4 -f in.gro -o out.gro

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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