[gmx-users] micelle clustering

[gregory megariotis]

Dear Sulatha, 

You can try the command trjconv -f a.xtc -o
b.gro -pbc cluster -e 0.002 with GROMACS 4.5.4. 

Best regrds 

Grigoris

--- Στις Πέμ., 30/06/11, ο/η sulatha M. S <mssulatha at gmail.com> έγραψε:

Από: sulatha M. S <mssulatha at gmail.com>
Θέμα: [gmx-users] micelle clustering
Προς: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Ημερομηνία: Πέμπτη, 30 Ιούνιος 2011, 9:18





Hi all,
I have simulated a system of randomly dispersed surfactants in
water using gromacs (4.0.7) for about 100 ns MD. Micelles are formed after
around 40 ns.  I am using a time step of
0.002 fs with xtc files written every 500 steps. For analyzing the micellar
properties, I tried the commands given in 

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

and also looked at the various posts given on this topic, (specifically
Chris Neale’s and Tsjerk’s mails).

As posted by Chris Neale, I tried using the commands,

1. trjconv -f a.xtc -o b.gro -pbc cluster -e 0.001 (make sure to just  get one frame)2. grompp -f a.mdp -c b.gro -p a.top -o b.tpr3. trjconv -f a.xtc -o b.xtc -s b.tpr -pbc nojump


 

Also mentioned in Tsjerk’ post that

“When doing so, be sure to use a frame which is close enough to thestarting frame in terms of the coordinates. -pbc nojump works based onthe coordinates and if you use a reference which doesn't match the
starting frame close enough everything can get really messed up”.  

I tried the command 1 with 

 trjconv -f a.xtc -o
b.gro -pbc cluster -e 0.002 

and also

 trjconv -f a.xtc -o
b.gro -pbc cluster –dump X (where x=2, 4, 6, 8 etc..)

The program gets into a never ending loop. 

I also tried the command 1 on a later part of the trajectory
(after 40 ns), there also the program enters in a indefinite loop.

I will greatly appreciate any help on how to go about doing
this specifically which frame (for dump or –e argument) .  Please guide me on this.

I also downloaded the modified trjconv.c  by Tsjerk (in one of his posts on micelle
clustering), but do not know where to incorporate this. I need some help on how
to use this modified trjconv code.
Thanks for any help or clue,
Sulatha



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