-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.
_______________________________________________
gmx-users mailing list [email protected]
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
