[gmx-users] g_dist error
aiswarya pawar
aiswarya.pawar at gmail.com
Tue Sep 13 10:02:26 CEST 2011
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.Abraham at 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.Abraham at 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.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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>>
>>
>>
>>
>>
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