On 13/09/2011 3:40 PM, aiswarya pawar wrote:
Hi Mark,
The -dist option says- print all the atoms in group 2 that are closer
than a certain distance to the center of mass of group 1.
That means it should give me the distance from OW to protein atom.
If you choose correct groups that are correctly defined with respect to
your trajectory and use a large enough distance cutoff.
And when am already specifying only one atom from protein ie say 1322.
why do i get this kind of output-
We can't tell. We don't know what your command line is, what's in your
simulation system, the contents of your index groups, or which groups
you've selected for which role. Clearly something is not working
properly, and our time constraints mean that we're going to assume
you've done something wrong, in the absence of evidence to the contrary.
Mark
t: 275 20230 SOL 62618 OW 0.341434 (nm)
t: 275 22019 SOL 67985 OW 0.171584 (nm)
t: 276 10768 SOL 34232 OW 0.303328 (nm)
t: 276 20230 SOL 62618 OW 0.325176 (nm)
t: 276 22019 SOL 67985 OW 0.187259 (nm)
t: 277 10768 SOL 34232 OW 0.306008 (nm)
t: 277 20230 SOL 62618 OW 0.326195 (nm)
t: 277 22019 SOL 67985 OW 0.181089 (nm)
t: 278 10768 SOL 34232 OW 0.274507 (nm)
t: 278 22019 SOL 67985 OW 0.292652 (nm)
t: 279 10618 SOL 33782 OW 0.319922 (nm)
t: 280 10618 SOL 33782 OW 0.330082 (nm)
t: 280 22019 SOL 67985 OW 0.330203 (nm)
t: 281 8273 SOL 26747 OW 0.278731 (nm)
t: 281 10618 SOL 33782 OW 0.325434 (nm)
t: 281 11535 SOL 36533 OW 0.200327 (nm)
t: 281 17036 SOL 53036 OW 0.343946 (nm)
t: 282 8273 SOL 26747 OW 0.256558 (nm)
t: 282 11535 SOL 36533 OW 0.327147 (nm)
t: 283 8273 SOL 26747 OW 0.165061 (nm)
t: 283 10618 SOL 33782 OW 0.306578 (nm)
t: 283 17191 SOL 53501 OW 0.333075 (nm)
t: 284 8273 SOL 26747 OW 0.19427 (nm)
t: 284 10618 SOL 33782 OW 0.321927 (nm)
t: 284 17191 SOL 53501 OW 0.30832 (nm)
On Tue, Sep 13, 2011 at 10:40 AM, Mark Abraham
<mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>> wrote:
On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com
<mailto:aiswarya.pa...@gmail.com> wrote:
Iam -dist option because I need the distance between two groups
That is not what g_dist -dist does. Please read g_dist -h.
excluding -dist gives me X,Y,Z output which I don't want.
And other output which you do, but you have to use -o to get it.
Read g_dist -h.
And am not specifying an -o.
You need to specify -o to achieve your purpose. However, as I said
quite a while ago, there is no value in measuring the distance
between a protein phase and a water phase if they are in contact...
Mark
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for
it!
-----Original Message-----
From: "Justin A. Lemkul"<jalem...@vt.edu> <mailto:jalem...@vt.edu>
Date: Mon, 12 Sep 2011 22:35:28
To:<aiswarya.pa...@gmail.com> <mailto:aiswarya.pa...@gmail.com>; Discussion list for
GROMACS users<gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org>
Reply-To:jalem...@vt.edu <mailto:jalem...@vt.edu>
Subject: Re: [gmx-users] g_dist error
aiswarya.pa...@gmail.com <mailto:aiswarya.pa...@gmail.com> wrote:
Even if I specify an atom say 1277 atom number to find distance against the
OW atoms. I get the same result of SOL-OW distance. Is it a bug cause even
after specifying one atom from a protein why doesn't it give me the result for
the SOL.
As was suggested several messages ago, please do NOT combine -o and -dist.
If
you want to measure a distance, use -o. If you want g_dist to print a list
of
atoms that satisfy some given criteria, use -dist, but not together.
-Justin
Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for
it!
-----Original Message-----
From: "Justin A. Lemkul"<jalem...@vt.edu> <mailto:jalem...@vt.edu>
Sender:gmx-users-boun...@gromacs.org <mailto:gmx-users-boun...@gromacs.org>
Date: Mon, 12 Sep 2011 07:52:54
To: Discussion list for GROMACS users<gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org>
Reply-To:jalem...@vt.edu <mailto:jalem...@vt.edu>,
Discussion list for GROMACS users<gmx-users@gromacs.org>
<mailto:gmx-users@gromacs.org>
Subject: Re: [gmx-users] g_dist error
aiswarya pawar wrote:
hi Justin,
As far i referred the OW,HW1 etc are water atoms so how can it be
distance between the SOL protein atoms, instead it is SOL water atoms.
The printed distance indicates that there is a certain water molecule that
is
just over 2 hydrogen bonding lengths away from your protein's backbone.
Sounds
normal to me.
-Justin
Thanks
On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul<jalem...@vt.edu
<mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu>> wrote:
aiswarya pawar wrote:
Hi Users,
Am using g_dist to find the distance between water and protein.
but my output has the values of SOL-water distance.
t: 1 136 SOL 2336 OW 0.772373 (nm)
This is not a water-water distance, it is the output of the -dist
option telling you that water molecule 136 has its OW atom at
0.7723273 nm from whatever your reference group is.
-Justin
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
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