[gmx-users] Position restraint doesn't work

David van der Spoel spoel at xray.bmc.uu.se
Sun Jan 2 10:53:09 CET 2005

On Sat, 1 Jan 2005 asaraujo at if.sc.usp.br wrote:

>Yes... the cohesion is smaller in acetonitrile than water, but I don't think
>it's SO far... whatever...
>What do you mean about the position restraint still be a problem with
>periodicity??? Are you suggesting me to aply the position restraint in a box
>with periodicity and see if it works? I didn't do this yet, but I'll do...
>But..do you agree that position restraint shoul work in my system? Or do you
>think that this simulation of a sphere can generate problems???

What I mean is that you may have a periodic box with a sphere inside and 
that the molecules wrap around, which is not a problem, but thay seem to 
be far off. To implement proper sphere in vacuum you want to set
pbc = no
all cutoff to 0 (i.e. no cutoffs)
and nstlist = 0
nstcomm = 1
comm_mode = angular

If you do want cut/offs you needs to set (e.g.)
cutoffs = 1
nstlist = 5

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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