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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