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<br><br>
<div class="gmail_quote">On Sun, Sep 20, 2009 at 8:02 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im"><br><br>Jamie Seyed wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Thanks Mark,<br>here are the links.<br><a href="http://www.psc.edu/general/software/packages/gromacs/online/water.html" target="_blank">http://www.psc.edu/general/software/packages/gromacs/online/water.html</a><br>
<a href="http://www.mail-archive.com/gmx-users@gromacs.org/msg07653.html" target="_blank">http://www.mail-archive.com/gmx-users@gromacs.org/msg07653.html</a><br> I tried your advice with 1 water molecule and since it worked I tried it with SOL.ndx, but I got<br>
D[SOL] -0.0333(+/- 0.0370) 1e-5 cm^2/s<br>It seems not reasonable to me (negative and its error is bigger than itself). Any idea?<br></blockquote><br></div>Probably inadequate sampling, either from the number of frames saved, or from the length of the simulation itself.<br>
<br>-Justin<br><br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">Thanks in Advance/Jamie
<div>
<div></div>
<div class="h5"><br><br>On Sun, Sep 20, 2009 at 7:02 PM, Mark Abraham <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>> wrote:<br>
<br> Jamie Seyed wrote:<br><br> Hi Mark,<br> Thanks for the puzzling answer. I tried the index file counting<br> the number of water molecule but I got an error.<br> "Fatal error:<br> The index group does not consist of whole molecules"<br>
<br><br> OK so apparently it wants atom indices for whole molecules. That<br> seems much more plausible to me than David's advice you quoted<br> (please give URLs to such quotes in future, perhaps you took it out<br>
of context...)<br><br> So try giving it atom indices for a whole water molecule as an<br> experiment. Seems like an obvious try to me :-) Then, scale it up if<br> it seems to work.<br><br><br> I also did not understand what you pointed out about "One of<br>
these sets of numbers is larger than the other" ...<br><br><br> One of the set of atom indices in a protein and the set of molecule<br> indices in a solvated protein will have more members than the other.<br>
Instead of asking which is right, you might try out a case that will<br> fail under one assumption and work under the other :-) Then perhaps<br> ask a question with some evidence behind it.<br><br><br> questions:<br>
1) for msd calculation for water molecules, do I need really<br> make index file for all waters,<br> 2) What I made (count the water molecules in a [mymolecules]<br> index file), did not work. How I suppose to do make that?<br>
3) In getting started-Water page that I found in google it only<br> say "g_msd -n index" and did not explain which index... how<br> about if I use oxygen.ndx file??<br><br><br> Provide links, please. We're not going to duplicate your googling.<br>
<br> Mark<br><br> I really appreciate your help. Many Thanks in Advance/Jamie<br><br><br><br> On Sun, Sep 20, 2009 at 3:33 PM, Mark Abraham<br> <<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>><br>
<mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a><br> <mailto:<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>>>> wrote:<br>
<br> Jamie Seyed wrote:<br><br> Dear all,<br> I want to calculate the msd using g_msd. I have a<br> macromolecule<br> and some (let say 100) water molecules and I want to use<br>
msd for<br> water only. from the manual and list I think I need to<br> make an<br> index for molecules (water) and use -mol option.<br> From David's answer on the list I found<br>
-----------------------------------------------------<br> "If you know which molecules they are then you just write<br> in a<br> text editor:<br> [ mymolecules ]<br>
3 5 19 23 45 109"<br> ----------------------------------------------------<br> My question is: let say the macromolecule is coming first<br> in the<br> pdb file and then there are water molecules. If I want to<br>
make<br> an index for only waters, according to this advice, should I<br> write 2 3 4... 100 (just remove 1 that goes for<br> macromolecule)<br> I am wondering if there is a confliction between these<br>
numbers(refer to molecules) and atom numbers of<br> macromolecule.... Would you please clarify this for me??<br><br><br> Try it and see. One of these sets of numbers is larger than the<br>
other, and if you use a number in that interval you'll either<br> get an<br> error or success, either of which will answer your question.<br><br> Mark<br> _______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
</div></div> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a> <mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>>>
<div>
<div></div>
<div class="h5"><br><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br> Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br>
posting!<br> Please don't post (un)subscribe requests to the list. Use the www<br> interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>><br> <mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>>.<br><br> Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br><br><br> ------------------------------------------------------------------------<br><br><br><br> _______________________________________________<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a><br> before posting!<br> Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br> <mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br><br> _______________________________________________<br> gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before<br> posting!<br> Please don't post (un)subscribe requests to the list. Use the www<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br> <mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br><br><br><br>------------------------------------------------------------------------<br>
<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></div></div></blockquote><br>-- <br>========================================<br>
<br>Justin A. Lemkul<br>Ph.D. Candidate<br>ICTAS Doctoral Scholar<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a href="http://vt.edu/" target="_blank">vt.edu</a> | (540) 231-9080<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>========================================
<div>
<div></div>
<div class="h5"><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br></div></div></blockquote></div><br>