Hi Mark, Thanks for the puzzling answer. I tried the index file counting the number of water molecule but I got an error. "Fatal error: The index group does not consist of whole molecules" I also did not understand what you pointed out about "One of these sets of numbers is larger than the other" ... questions: 1) for msd calculation for water molecules, do I need really make index file for all waters, 2) What I made (count the water molecules in a [mymolecules] index file), did not work. How I suppose to do make that? 3) In getting started-Water page that I found in google it only say "g_msd -n index" and did not explain which index... how about if I use oxygen.ndx file?? I really appreciate your help. Many Thanks in Advance/Jamie
On Sun, Sep 20, 2009 at 3:33 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > Jamie Seyed wrote: > >> 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?? >> > > Try it and see. One of these sets of numbers is larger than the other, and > if you use a number in that interval you'll either get an error or success, > either of which will answer your question. > > Mark > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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