Yes Thanks Justin, should I just use the linear part of msd for fit even if it is short (like 14ps from 200ps)? Thanks/Jamie
On Sun, Sep 20, 2009 at 8:02 PM, Justin A. Lemkul <[email protected]> wrote: > > > Jamie Seyed wrote: > >> Thanks Mark, >> here are the links. >> http://www.psc.edu/general/software/packages/gromacs/online/water.html >> http://www.mail-archive.com/[email protected]/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? >> > > Probably inadequate sampling, either from the number of frames saved, or > from the length of the simulation itself. > > -Justin > > Thanks in Advance/Jamie >> >> >> On Sun, Sep 20, 2009 at 7:02 PM, Mark Abraham >> <[email protected]<mailto: >> [email protected]>> 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 >> <[email protected] <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>> 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 [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>> >> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/searchbefore >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www >> interface or send it to [email protected] >> <mailto:[email protected]> >> <mailto:[email protected] >> <mailto:[email protected]>>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> ------------------------------------------------------------------------ >> >> >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> 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 [email protected] >> <mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> <mailto:[email protected]> >> 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 [email protected] >> <mailto:[email protected]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list [email protected] >> 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 [email protected]. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > _______________________________________________ > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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