[gmx-users] g_dist error
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Sep 13 09:54:29 CEST 2011
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 <mailto: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 <mailto:Mark.Abraham at anu.edu.au>> wrote:
>>
>> On 13/09/2011 2:27 PM, aiswarya.pawar at gmail.com
>> <mailto: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> <mailto:jalemkul at vt.edu>
>>> Date: Mon, 12 Sep 2011 22:35:28
>>> To:<aiswarya.pawar at gmail.com> <mailto:aiswarya.pawar at gmail.com>; Discussion list for GROMACS users<gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org>
>>> Reply-To:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>>> Subject: Re: [gmx-users] g_dist error
>>>
>>>
>>>
>>> aiswarya.pawar at gmail.com <mailto: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> <mailto:jalemkul at vt.edu>
>>>> Sender:gmx-users-bounces at gromacs.org <mailto: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> <mailto:gmx-users at gromacs.org>
>>>> Reply-To:jalemkul at vt.edu <mailto:jalemkul at vt.edu>,
>>>> Discussion list for GROMACS users<gmx-users at gromacs.org> <mailto: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>
>>>>> <mailto: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>
>>>>>
>>>>> ==============================__==========
>>>>> --
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