[gmx-users] g_dist error

aiswarya pawar aiswarya.pawar at gmail.com
Tue Sep 13 07:40:13 CEST 2011 

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.

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)
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.Abraham at anu.edu.au>wrote:

>  On 13/09/2011 2:27 PM, aiswarya.pawar at 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" <jalemkul at vt.edu> <jalemkul at vt.edu>
> Date: Mon, 12 Sep 2011 22:35:28
> To: <aiswarya.pawar at gmail.com> <aiswarya.pawar at gmail.com>; Discussion list for GROMACS users<gmx-users at gromacs.org> <gmx-users at gromacs.org>
> Reply-To: jalemkul at vt.edu
> Subject: Re: [gmx-users] g_dist error
>
>
> aiswarya.pawar at 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" <jalemkul at vt.edu> <jalemkul at vt.edu>
> Sender: gmx-users-bounces at gromacs.org
> Date: Mon, 12 Sep 2011 07:52:54
> To: Discussion list for GROMACS users<gmx-users at gromacs.org> <gmx-users at gromacs.org>
> Reply-To: jalemkul at vt.edu,
> 	Discussion list for GROMACS users <gmx-users at gromacs.org> <gmx-users at 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 <jalemkul at vt.edu <mailto:jalemkul at vt.edu> <jalemkul at 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>
>
>     ==============================__==========
>     --
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