[gmx-users] problem with trjconv -pbc cluster

[jagannath mondal]

Thanks for the reply. I used following command to extract first frame that has all the surfectants ( as suggested by first step for characterizing micelle clustering).
   trjconv -f a.xtc -o a_cluster.gro -dump 0 -pbc cluster Here is the output I got:COM:    0.000     0.000    19.999  iter = 19526  Isq = 12671033.000COM:    0.000     0.000     0.000  iter = 19527  Isq = 12628369.000COM:    0.000     0.000    19.999  iter = 19528  Isq = 12671033.000COM:    0.000     0.000     0.000  iter = 19529  Isq = 12628369.000COM:    0.000     0.000    19.999  iter = 19530  Isq = 12671033.000COM:    0.000     0.000     0.000  iter = 19531  Isq = 12628369.000COM:    0.000     0.000    19.999  iter = 19532  Isq = 12671033.000COM:    0.000     0.000     0.000  iter = 19533  Isq = 12628369.000COM:    0.000     0.000    19.999  iter = 19534  Isq = 12671033.000COM:    0.000     0.000     0.000  iter = 19535  Isq = 12628369.000COM:    0.000     0.000    19.999  iter = 19536  Isq = 12671033.000COM:    0.000     0.000     0.000  iter = 19537
  Isq = 12628369.000COM:    0.000     0.000    19.999  iter = 19538  Isq = 12671033.000
looks like lsq is only fluctuating between two numbers and the program is in an infinte loop. 
Jagannath 
--- On Wed, 7/7/10, Mark Abraham <mark.abraham at anu.edu.au> wrote:

From: Mark Abraham <mark.abraham at anu.edu.au>
Subject: Re: [gmx-users] problem with trjconv -pbc cluster
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Date: Wednesday, 7 July, 2010, 12:20 PM



----- 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

> 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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