[gmx-users] problem with trjconv -pbc cluster

[Mark Abraham]

----- Original Message -----
From: jagannath mondal <jmondal2004 at yahoo.co.in>
Date: Wednesday, July 7, 2010 16:36
Subject: [gmx-users] problem with trjconv -pbc cluster
To: gmx-users at gromacs.org

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| > 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:>  http://www.gromacs.org/Documentation/How-tos/Micelle_Clustering> 
> 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 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


> 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 convergence.

So what command did you give, what output did you get, and does the command make sense with respect to your trajectory contents?

Mark

> 
> I am using gromacs 4.0.7> 
> Any help will be appreciated.> 
> Jagannath |
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