D D wrote:
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.
Look at the routine trjconv -pbc mol is using.
Mark
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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