On 12/24/2011 8:01 PM, mohammad agha wrote:
Dear GROMACS users
I want to analysis of 2 micelles that are created in one simulation,
when I view output of trajectory by vmd or ngmx:
ngmx -f md.trr -s md.tpr
has been created 2 micelles, then I try to micelle clustering by:
1. |trjconv -f md.xtc -o a_cluster.gro -e 0.001 -pbc cluster|
2. |grompp -f md.mdp -c a_cluster.gro -o a_cluster.tpr|
3. |trjconv -f md.xtc -o a_cluster.xtc -s a_cluster.tpr -pbc nojump|
but when I view cluster.xtc, just has been created one micelles and
remainder of monomers have been collected in different places in 3 or
4 groups!!!
May I know why do this occur? and where is my mistake? and what should
I do, please?
Hard to say, because we don't know what your objective is. You need to
be very clear in your own mind what you want to see if the underlying
behaviour is that the two micelles move away from each other in one cell
and meet each other across another boundary, and design a workflow
accordingly.
I suggest you read trjconv -h carefully and consider the workflow advice
here
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Mark
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