[gmx-users] micelle clustering

[sulatha M. S]

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.tpr

3. 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 the

starting frame in terms of the coordinates. -pbc nojump works based on

the 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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