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>> 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>>> 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
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--
========================================
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
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