Dear all, I want to calculate the msd using g_msd. I have a macromolecule and some (let say 100) water molecules and I want to use msd for water only. from the manual and list I think I need to make an index for molecules (water) and use -mol option. >From David's answer on the list I found ----------------------------------------------------- "If you know which molecules they are then you just write in a text editor: [ mymolecules ] 3 5 19 23 45 109" ---------------------------------------------------- My question is: let say the macromolecule is coming first in the pdb file and then there are water molecules. If I want to make an index for only waters, according to this advice, should I write 2 3 4... 100 (just remove 1 that goes for macromolecule) I am wondering if there is a confliction between these numbers(refer to molecules) and atom numbers of macromolecule.... Would you please clarify this for me?? Many Thanks in advance/Jamie
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