<div dir="ltr">To specify a bit. Lets say I have a normal trajectory that looks like this: reftraj.xyz Cryst x i = 0, time = 0.000, E = -16.1066791009 O 4.4494725764 0.8609855793 6.0981987308 O 3.8029095709 2.7229831166 4.5699381898 O 4.0118989226 2.7023681308 1.2194938263 O 6.0462348498 3.2953089592 5.9203028333 O 3.2241009956 5.5031225318 4.3400008035 .. .. .. with 1000 steps inside. Now I want to calculate the MSD with reference to the first configuration, how do I do that? If I do this &MOTION &MD STEPS 1000 TIMESTEP 1 ENSEMBLE REFTRAJ &REFTRAJ TRAJ_FILE_NAME reftraj.xyz FIRST_SNAPSHOT 1 LAST_SNAPSHOT 1000 &PRINT &MSD_KIND &END MSD_KIND &END PRINT &MSD T &MSD_PER_KIND &END MSD_PER_KIND &END MSD &END REFTRAJ &END MD &END MOTION I only get this error ************************************************************* *** ERROR in initialize_msd_reftraj (MODULE reftraj_util) *** ************************************************************* *** End of reference positions file reached *** however there are definitly 1000 steps in the file I link.. Anything else I need to consider? My question still stand if I can do this during the an ordinary MD run.. so not calculating the trajectory first and then letting the reftraj code run over it but have it as a normal output at the end of the run. Thanks again and best regards, Johannes </div>