[CP2K-user] [CP2K:19961] After running AIMD, how to define molecule kind for MSD calculation via REFTRAJ?

[jiaming li]

Dear all,

I have done SGCPMD simulation and get pdb file as trajectory. Is it 
possible to define a list of atoms in pdb file as a molecule and use 
MSD_PER_MOLKIND to calculate mean square displacement for that molecule?

&GLOBAL
PROJECT msd001
PRINT_LEVEL LOW
RUN_TYPE MD
&END GLOBAL

&MOTION
&MD
&REFTRAJ
TRAJ_FILE_NAME emi_cpmd-pos-1.pdb
FIRST_SNAPSHOT 12000
LAST_SNAPSHOT 95818
STRIDE 1
REF0_FILENAME initial-emi.pdb
&MSD
MSD_PER_MOLKIND T
&END MSD
&END REFTRAJ
&END MD
&END MOTION

Thanks,
Jiaming

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