g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500 if the index name not given it takes the default index file, so there isnt any wrong in selecting the atoms.<br><br><div class="gmail_quote">On Tue, Sep 13, 2011 at 1:24 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div bgcolor="#FFFFFF" text="#000000"><div class="im">
On 13/09/2011 4:14 PM, aiswarya pawar wrote:
<blockquote type="cite">Mark,<br>
<br>
the command line goes like this-<br>
<br>
g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500<br>
</blockquote>
<br></div>
This command line is not using an index file. The index groups
defined for the grompp that produced the .tpr are being used (which
may be the default ones, depending what you did). Please copy and
show the interactive input you made to g_dist after it showed the
groups it knew about.<div class="im"><br>
<br>
<blockquote type="cite"><br>
the index file has group1- a_1322 ( this is just a single atom
from a protein. its in sidechain)<br>
group2- a_OW ( this is water atoms)<br>
</blockquote>
<br></div>
Your output is listing the time of the frame, and the residue
number, residue name, atom number, and atom name of the matching
atom. Apparently a water molecule can sometimes be closer than
0.2nm, and sometimes not.<br><font color="#888888">
<br>
Mark</font><div><div></div><div class="h5"><br>
<br>
<blockquote type="cite">
<br>
now as per the utility it should give me and output as-<br>
<br>
t:1 1322 a 54119 OW 0.389<br>
<br>
but am getting something different<br>
<br>
<div class="gmail_quote">On Tue, Sep 13, 2011 at 11:24 AM, Mark
Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div bgcolor="#FFFFFF" text="#000000">
<div> On 13/09/2011 3:40 PM, aiswarya pawar
wrote:
<blockquote type="cite"><br>
Hi Mark,<br>
<br>
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.<br>
That means it should give me the distance from OW to
protein atom.<br>
</blockquote>
<br>
</div>
If you choose correct groups that are correctly defined with
respect to your trajectory and use a large enough distance
cutoff.
<div><br>
<br>
<blockquote type="cite"><br>
And when am already specifying only one atom from
protein ie say 1322. why do i get this kind of output-<br>
</blockquote>
<br>
</div>
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.<br>
<font color="#888888"> <br>
Mark</font>
<div>
<div><br>
<br>
<blockquote type="cite"> <br>
t: 275 20230 SOL 62618 OW 0.341434 (nm)<br>
t: 275 22019 SOL 67985 OW 0.171584 (nm)<br>
t: 276 10768 SOL 34232 OW 0.303328 (nm)<br>
t: 276 20230 SOL 62618 OW 0.325176 (nm)<br>
t: 276 22019 SOL 67985 OW 0.187259 (nm)<br>
t: 277 10768 SOL 34232 OW 0.306008 (nm)<br>
t: 277 20230 SOL 62618 OW 0.326195 (nm)<br>
t: 277 22019 SOL 67985 OW 0.181089 (nm)<br>
t: 278 10768 SOL 34232 OW 0.274507 (nm)<br>
t: 278 22019 SOL 67985 OW 0.292652 (nm)<br>
t: 279 10618 SOL 33782 OW 0.319922 (nm)<br>
t: 280 10618 SOL 33782 OW 0.330082 (nm)<br>
t: 280 22019 SOL 67985 OW 0.330203 (nm)<br>
t: 281 8273 SOL 26747 OW 0.278731 (nm)<br>
t: 281 10618 SOL 33782 OW 0.325434 (nm)<br>
t: 281 11535 SOL 36533 OW 0.200327 (nm)<br>
t: 281 17036 SOL 53036 OW 0.343946 (nm)<br>
t: 282 8273 SOL 26747 OW 0.256558 (nm)<br>
t: 282 11535 SOL 36533 OW 0.327147 (nm)<br>
t: 283 8273 SOL 26747 OW 0.165061 (nm)<br>
t: 283 10618 SOL 33782 OW 0.306578 (nm)<br>
t: 283 17191 SOL 53501 OW 0.333075 (nm)<br>
t: 284 8273 SOL 26747 OW 0.19427 (nm)<br>
t: 284 10618 SOL 33782 OW 0.321927 (nm)<br>
t: 284 17191 SOL 53501 OW 0.30832 (nm)<br>
<br>
<br>
<br>
<br>
<div class="gmail_quote">On Tue, Sep 13, 2011 at 10:40
AM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div bgcolor="#FFFFFF" text="#000000">
<div> On 13/09/2011 2:27 PM, <a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a>
wrote:
<blockquote type="cite">
<pre>Iam -dist option because I need the distance between two groups</pre>
</blockquote>
<br>
</div>
That is not what g_dist -dist does. Please read
g_dist -h.
<div><br>
<br>
<blockquote type="cite">
<pre> excluding -dist gives me X,Y,Z output which I don't want.</pre>
</blockquote>
<br>
</div>
And other output which you do, but you have to
use -o to get it. Read g_dist -h.
<div><br>
<br>
<blockquote type="cite">
<pre> And am not specifying an -o.</pre>
</blockquote>
<br>
</div>
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...<br>
<font color="#888888"> <br>
Mark</font>
<div>
<div><br>
<br>
<blockquote type="cite">
<pre>Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
-----Original Message-----
From: "Justin A. Lemkul" <a href="mailto:jalemkul@vt.edu" target="_blank"><jalemkul@vt.edu></a>
Date: Mon, 12 Sep 2011 22:35:28
To: <a href="mailto:aiswarya.pawar@gmail.com" target="_blank"><aiswarya.pawar@gmail.com></a>; Discussion list for GROMACS users<a href="mailto:gmx-users@gromacs.org" target="_blank"><gmx-users@gromacs.org></a>
Reply-To: <a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>
Subject: Re: [gmx-users] g_dist error
<a href="mailto:aiswarya.pawar@gmail.com" target="_blank">aiswarya.pawar@gmail.com</a> wrote:
</pre>
<blockquote type="cite">
<pre>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.
</pre>
</blockquote>
<pre>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
</pre>
<blockquote type="cite">
<pre>Thanks
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
-----Original Message-----
From: "Justin A. Lemkul" <a href="mailto:jalemkul@vt.edu" target="_blank"><jalemkul@vt.edu></a>
Sender: <a href="mailto:gmx-users-bounces@gromacs.org" target="_blank">gmx-users-bounces@gromacs.org</a>
Date: Mon, 12 Sep 2011 07:52:54
To: Discussion list for GROMACS users<a href="mailto:gmx-users@gromacs.org" target="_blank"><gmx-users@gromacs.org></a>
Reply-To: <a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>,
Discussion list for GROMACS users <a href="mailto:gmx-users@gromacs.org" target="_blank"><gmx-users@gromacs.org></a>
Subject: Re: [gmx-users] g_dist error
aiswarya pawar wrote:
</pre>
<blockquote type="cite">
<pre>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.
</pre>
</blockquote>
<pre>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
</pre>
<blockquote type="cite">
<pre>Thanks
On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>
<a href="mailto:jalemkul@vt.edu" target="_blank"><mailto:jalemkul@vt.edu></a>> 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]<a href="http://vt.edu" target="_blank">vt.edu</a> <a href="http://vt.edu" target="_blank"><http://vt.edu></a> | (540) 231-9080
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