Greetings,
My system is composed of a two-phase liquid (aqueous solution and an organic phase) confined between two solid surfaces. When I directly use the atom coordinates (from the dump files) to calculate MSD, the obtained values are different from the output of the “compute msd” command. The manually-calculated MSD curves (of the liquid molecules) reach a plateau after about 20 ns. However, based on the outputs of the command, only in z direction it exhibits a plateau, while it monotonously increases with time along x and y direction (so overall it has a rising trend with time). Is this discrepancy caused by the coordinates being wrapped in the dump files? I’d appreciate your comments.
Best regards,
Monir
Greetings,
My system is composed of a two-phase liquid (aqueous solution and an organic phase) confined between two solid surfaces. When I directly use the atom coordinates (from the dump files) to calculate MSD, the obtained values are different from the output of the “compute msd” command. The manually-calculated MSD curves (of the liquid molecules) reach a plateau after about 20 ns. However, based on the outputs of the command, only in z direction it exhibits a plateau, while it monotonously increases with time along x and y direction (so overall it has a rising trend with time). Is this discrepancy caused by the coordinates being wrapped in the dump files? I’d appreciate your comments.
that is difficult to answer since, a) we don’t know what exactly you are outputting in your dump files and b) how well your external program is written.
what you describe as the result from compute msd is what i would expect for the kind of geometry you mention.
axel.