Hi *,<br>I wrote a tool to calculate properties from trajectories (parallel 4.0.5), but it seems that I miss something.<br>In the case of MSD, I do not get the curve that g_msd produces for mol com.<br>On the other hand, if I run this tool for MSD on a trajectory produced by trjconv -pbc mol,<br>
I get the right curve (I handle pbc jumps of com after calc_xcm).<br>I think that the problem comes from pbc handling for molecules splited across boundaries - I expect : do something before calc_xcm.<br>I could run trjconv before run tool, but I &#39;d like to use the original trajectories and handle them correctly.<br>
Any suggestion is appreciable.<br><br>The procedure I follow is :<br>read_tps_conf<br>read_first_frame<br>do { <br>prepare_index_etc<br>calc_xcm<br>do_some_calculations_here<br>}while (read_next_frame)<br><br>Thanks<br>DD<br>
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