never used the -dist option, but i think you have here a missunderstanding:
>>> t: 275 20230 SOL 62618 OW 0.341434 (nm)
i think this means: at time=275 atom 62618 (which is a OW) from residue
20230 (which is a SOL) is 0.341434nm away from your protein atom.
the x SOL y OW means not the distance between some SOl-atom and OW, but
that the OW atom is from the residue x from the SOL group!!!
>>> And when am already specifying only one atom from protein ie say
1322. why
>>> do i get this kind of output-
>>> 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)
...
you get this output, because the programm assumes that you remember
which was group 1 and so it does not need to write it in every line.
since i never used the -dist option, the stuff above could be false, so
short thing you can do is and look if atom 62618 is in residue 20230,
and then the above should be right.
greetings
thomas
Date: Tue, 13 Sep 2011 13:32:26 +0530
From: aiswarya pawar<aiswarya.pa...@gmail.com>
Subject: Re: [gmx-users] g_dist error
To: Discussion list for GROMACS users<gmx-users@gromacs.org>
Message-ID:
<CAEa6cRA+7W5Hed_KHtPN3cqmPD8xyE5ZJrS-HSap6-2C6h2=9...@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
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.
On Tue, Sep 13, 2011 at 1:24 PM, Mark Abraham<mark.abra...@anu.edu.au>wrote:
On 13/09/2011 4:14 PM, aiswarya pawar wrote:
Mark,
the command line goes like this-
g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500
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.
the index file has group1- a_1322 ( this is just a single atom from a
protein. its in sidechain)
group2- a_OW ( this is water atoms)
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.
Mark
now as per the utility it should give me and output as-
t:1 1322 a 54119 OW 0.389
but am getting something different
On Tue, Sep 13, 2011 at 11:24 AM, Mark Abraham<mark.abra...@anu.edu.au>wrote:
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>wrote:
On 13/09/2011 2:27 PM, 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> <jalem...@vt.edu>
Date: Mon, 12 Sep 2011 22:35:28
To:<aiswarya.pa...@gmail.com> <aiswarya.pa...@gmail.com>; Discussion list for GROMACS
users<gmx-users@gromacs.org> <gmx-users@gromacs.org>
Reply-To: jalem...@vt.edu
Subject: Re: [gmx-users] g_dist error
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> <jalem...@vt.edu>
Sender: gmx-users-boun...@gromacs.org
Date: Mon, 12 Sep 2011 07:52:54
To: Discussion list for GROMACS users<gmx-users@gromacs.org>
<gmx-users@gromacs.org>
Reply-To: jalem...@vt.edu,
Discussion list for GROMACS users<gmx-users@gromacs.org>
<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> <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>
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
--
gmx-users mailing list gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org> <gmx-users@gromacs.org>
http://lists.gromacs.org/__mailman/listinfo/gmx-users
<http://lists.gromacs.org/mailman/listinfo/gmx-users>
<http://lists.gromacs.org/mailman/listinfo/gmx-users>
Please search the archive at
http://www.gromacs.org/__Support/Mailing_Lists/Search
<http://www.gromacs.org/Support/Mailing_Lists/Search>
<http://www.gromacs.org/Support/Mailing_Lists/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> <gmx-users-requ...@gromacs.org>.
Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
<http://www.gromacs.org/Support/Mailing_Lists>
<http://www.gromacs.org/Support/Mailing_Lists>
--
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/Support/Mailing_Lists/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/Support/Mailing_Lists
--
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/Support/Mailing_Lists/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/Support/Mailing_Lists
--
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/Support/Mailing_Lists/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/Support/Mailing_Lists
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
http://lists.gromacs.org/pipermail/gmx-users/attachments/20110913/23293b3e/attachment.html
------------------------------
--
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/Support/Mailing_Lists/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/Support/Mailing_Lists
