[gmx-users] problem with trjconv -pbc cluster

chris.neale at utoronto.ca chris.neale at utoronto.ca
Wed Jul 7 17:57:32 CEST 2010


you realize that trjconv -pbc cluster is never going to work unless  
you actually have a cluster, right? So you can't start this procedure  
near your initial dispersed state. You need to start at some time T  
where you actually do have a cluster. Then you can try -dump T, -dump  
(T+X), -dump (T+X*2), etc. Then you can follow the ides expressed  
below like running backwards with -pbc nojup to get the initial state.


--original message --

Dear Jagannath:

There is, as far as I know, no way to fix this. Here's what you should do.

1. Let the space between your timesteps be X ps.
2. Use trjconv -pbc cluster -dump X -o out.gro
2b. if that doesn't work, try trjconv -pbc cluster -dump (X*2) -o out.gro
2c. if that doesn't work, try trjconv -pbc cluster -dump (X*3) -o out.gro
(Note use real numbers for args to -dump).

Once you have a frame that works, you can run part 2 and 3 of that
wiki page by making a tpr based on the gro that worked -- and I think
that you'll need to run your trjconv -pbc mol starting from the frame
where clustering worked (e.g. -b X). Note that this second requirement
means that you may need to reverse the frames from your .xtc file so
that you can run in reverse time from a complete micelle through to
disassembly with -pbc nojump -- a for loop around trjconv will work
but inefficiently, you might be able to use -demux smartly here (I'm
not sure).

But then since you have 2 micelles you will need a starting box in
which they are both whole.... getting trickier. You should be aware
that the trjconv -pbc cluster is not the only way to do part 1 from
that wiki page. You could use trjconv -trans X Y Z and then make a new
.tpr and then run trjconv -pbc nojump and it would work if only you
knew which X Y Z to use (although trial and error may help you here

Sorry this is confusing, but this is a difficult thing to do and you
should expect to struggle with it for some time, so another questino
to ask yourself is "do I really need to do this?" If its just for
making a movie then you can use pbctools in vmd for that.


-- original message --

Hi,  I had a system of surfectants which are started with an initial
configuration where all of them are well dispersed. Visual study of
trajectory shows they start aggregating and finally form two discrete
micelles. To quantify this micelle clusterization, I tried to use the
suggestions present in the gromacs documentations:
i.e    use trjconv -pbc cluster to obtain a single frame that has all
of the lipids in the unit cell. This must be the first frame of your
trajectory. A similar frame from some previous timepoint will not
work.use grompp to make a new tpr file based on the frame that was
output from the step above.use trjconv -pbc nojump to produce the
desired trajectory using the newly produced tpr file.trjconv -f a.xtc
-o a_cluster.gro -e 0.001 -pbc clustergrompp -f a.mdp -c a_cluster.gro
-o a_cluster.tprtrjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr
-pbc nojump
But, The first step i.e. trjconv -pbc cluster does not work. Looks
like it is going through an infinite loop and is not stopping for
I am using gromacs 4.0.7
Any help will be appreciated.

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