[gmx-users] PBC in g_gyrate

Chris Neale chris.neale at utoronto.ca
Thu Jan 18 01:05:41 CET 2007

-pbc cluster is definately what you want. However, this is slow and doesn't always converge, 
so doing it on a trajectory takes a lot of time. If you want another option:

The post http://www.gromacs.org/pipermail/gmx-users/2007-January/025388.html suggests:

trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster
grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr
trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump

However, this is not going to work if your cluster forms/breaks/reforms during the simulation
because a monomer that breaks off, goes across the PBC, and then rejoins the cluster is not going
to rejoin the cluster after the -pbc nojump phase. In that case, -pbc cluster on the whole 
trajectory may be your only option. Note that the -pbc cluster spits out a lot of data so 
running trjconv > out.stdout 2> out.stderr will actually save a lot of time.
Just be sure to manage/delete these output files later as they may be very large.

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