<div>Dear all,</div>
<div>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.</div>
<div>From David's answer on the list I found</div>
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<div>"If you know which molecules they are then you just write in a text editor:<br>[ mymolecules ]<br>3 5 19 23 45 109"</div>
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<div>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)</div>
<div>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?? </div>
<div>Many Thanks in advance/Jamie</div>
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