Hi,
I have run a simulation using gromacs 4.0.7 with 50 copies of amphiphilic
surfactant ( in water) using Martini coarse-grained force-field. Mere
visualization of trajectories shows that starting with 50 discrete copies, they
gradually aggregate and finally two well-separated large micelles are formed.
But, my problem starts in quantifying the cluster-size-distributions .
Here is what I tried:
1. Initially, I was trying to directly use g_clustsize tools to calculate the
cluster-size distribution. Here is the command line I used :
g_clustsize -f traj.xtc -s topol.tpr -mol
But, It turned out that for all the time-frame, it gives me only single
cluster having all the molecules , giving a flat line in the time-evolution of
cluster-size.
This looks to be wrong as the starting configuration has all the 50 copies of
surfectatnt well dispersed( at least from visualization) and at the end of the
simulation the visualization shows two clusters. Here, since I am interested
in the molecules that is part of a cluster , hence I used -mol option. Without
this option also, I get almost all the atoms in a single cluster .
Then I tried
trjconv -pbc nojump -f traj.xtc -o traj_nojump.xtc
option to take care of periodicity. But, It does not change the result
g_clustsize_4mpi is giving: it always gives me only 1 cluster. use of -pbc
whole also gives me same result.
2. I also tried to play with cut-off in g_clustsize . Initially I was using
default cut-off value ( 0.35 nm) . I tried smaller value but result does not
change. The most awkward part is that even if I make cut-off distance 0 as
follows:
g_clustsize -f traj.xtc -cut 0.0 -s topol -mol
it still gives me a single cluster ! How can it be possible ? I am pretty sure
there is something wrong but not able to figure this out.
3. Later, I found that in gromacs, there is a description of how to determine
micelle clusters ( perhaps by Justin Lemkul ? )
Here is the steps it was recommended :
1. trjconv -f a.xtc -o a_cluster.gro -e 0.001 -pbc cluster
2. grompp -f a.mdp -c a_cluster.gro -o a_cluster.tpr
3. trjconv -f a.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump
But, when I tried the first step as follows:
trjconv -f traj.xtc -o traj_cluster.gro -dump 0 -pbc cluster,
it looks like it does not converge and enter an infinite loop: Here is an
excerpt of the output:
COM: 0.000 0.000 19.999 iter = 19526 Isq = 12671033.000
COM: 0.000 0.000 0.000 iter = 19527 Isq = 12628369.000
COM: 0.000 0.000 19.999 iter = 19528 Isq = 12671033.000
COM: 0.000 0.000 0.000 iter = 19529 Isq = 12628369.000
COM: 0.000 0.000 19.999 iter = 19530 Isq = 12671033.000
COM: 0.000 0.000 0.000 iter = 19531 Isq = 12628369.000
COM: 0.000 0.000 19.999 iter = 19532 Isq = 12671033.000
COM: 0.000 0.000 0.000 iter = 19533 Isq = 12628369.000
COM: 0.000 0.000 19.999 iter = 19534 Isq = 12671033.000
COM: 0.000 0.000 0.000 iter = 19535 Isq = 12628369.000
COM: 0.000 0.000 19.999 iter = 19536 Isq = 12671033.000
COM: 0.000 0.000 0.000 iter = 19537 Isq = 12628369.000
COM: 0.000 0.000 19.999 iter = 19538 Isq = 12671033.000
I am not sure why I am getting an infinite loop ( looks like lsq is only
fluctuating between two numbers). I also saw similar kind of report in the
gromacs mailing list , but no proper solution came to my sight .
Overall, none of the attempts is giving me an appreciable result?
Can someone help me on this so as to get right cluster size distribution ? Any
help will be appreciated.
Thanks
Sanku
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