Hello everyone, In my simulation, I want to calculate the MSD of COM of some molecules using *gmx msd* command.
>From the Gromacs manual, *For molecules consisting of more than one atom, ri can be taken as the center of mass positions of the molecules. In that case, you should use an index file with molecule numbers.* It seems that all i need to do is create an index file with molecule numbers. Following is my procedure: *echo 'res_com of resname Tf2N' | gmx select -s nvt-msd.tpr -on mol.ndx* *gmx msd -f nvt-msd.xtc -s nvt-msd.tpr -n mol.ndx -o msd-com* However, it does not produce the result what I want. The resulting msd-com.xvg is not the MSD of COM of Tf2N molecule. It seems that mol.ndx has not been recognize as molecule numbers. Is there anything I missed? -- Gong, Zheng Doctoral Candidate in Physical Chemistry School of Chemistry and Chemical Engineering Shanghai Jiao Tong University http://sun.sjtu.edu.cn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.