GROMACS modification: NO
I want to know if the Gromacs use the COM in the gmx msd? Because I get some different results. My procedure is as follows:
make an index file for an ion(PF6) useing gmx make_ndx
using the command:
gmx msd -f xxx.trr -s xxx.tpr -n index.ndx -b 0 -e 1 (just the 0-1ps for the selected one PF6 )
And I get the MSD at t=1.0ps of the one selected PF6.
I get the COM of the selected the PF6 using gmx traj at t=0, t=1.0ps, and I get the MSD via these COM. But the MSD produced by 2 step is different from the step 3 .
I want to know the reasons, Thank you so much!