Jamie Seyed wrote:
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
Yes, the linear portion of the graph should be used for MSD analysis. 200 ps is
somewhat short, but might be sufficient for water.
-Justin
On Sun, Sep 20, 2009 at 8:02 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> 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/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?
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
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
<mailto:mark.abra...@anu.edu.au
<mailto: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>
<mailto:mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>>
<mailto:mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>
<mailto: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>
<mailto:gmx-users@gromacs.org <mailto:gmx-users@gromacs.org>>
<mailto:gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org> <mailto: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>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>>
<mailto:gmx-users-requ...@gromacs.org
<mailto:gmx-users-requ...@gromacs.org>
<mailto: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
<mailto:gmx-users@gromacs.org>
<mailto: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>
<mailto: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
<mailto:gmx-users@gromacs.org>
<mailto: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>
<mailto: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
<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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
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
--
========================================
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 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
