[gmx-users] trajectory info

[D D]

Hi *,
I wrote a tool to calculate properties from trajectories (parallel 4.0.5),
but it seems that I miss something.
In the case of MSD, I do not get the curve that g_msd produces for mol com.
On the other hand, if I run this tool for MSD on a trajectory produced by
trjconv -pbc mol,
I get the right curve (I handle pbc jumps of com after calc_xcm).
I think that the problem comes from pbc handling for molecules splited
across boundaries - I expect : do something before calc_xcm.
I could run trjconv before run tool, but I 'd like to use the original
trajectories and handle them correctly.
Any suggestion is appreciable.

The procedure I follow is :
read_tps_conf
read_first_frame
do {
prepare_index_etc
calc_xcm
do_some_calculations_here
}while (read_next_frame)

Thanks
DD
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