Thanks Mark, here are the links. http://www.psc.edu/general/software/packages/gromacs/online/water.html
http://www.mail-archive.com/gmx-users@gromacs.org/msg07653.html I tried your advice with 1 water molecule and since it worked I tried it with SOL.ndx, but I got D[SOL] -0.0333(+/- 0.0370) 1e-5 cm^2/s It seems not reasonable to me (negative and its error is bigger than itself). Any idea? Thanks in Advance/Jamie On Sun, Sep 20, 2009 at 7:02 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > Jamie Seyed wrote: > >> 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" >> > > OK so apparently it wants atom indices for whole molecules. That seems much > more plausible to me than David's advice you quoted (please give URLs to > such quotes in future, perhaps you took it out of context...) > > So try giving it atom indices for a whole water molecule as an experiment. > Seems like an obvious try to me :-) Then, scale it up if it seems to work. > > I also did not understand what you pointed out about "One of these sets of >> numbers is larger than the other" ... >> > > One of the set of atom indices in a protein and the set of molecule indices > in a solvated protein will have more members than the other. Instead of > asking which is right, you might try out a case that will fail under one > assumption and work under the other :-) Then perhaps ask a question with > some evidence behind it. > > 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?? >> > > Provide links, please. We're not going to duplicate your googling. > > Mark > > 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<mailto: >> 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 >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 >> > _______________________________________________ > 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 >
_______________________________________________ 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
