Mark,
the command line goes like this-
g_dist -f md.xtc -s md.tpr -dist 0.5 -e 500
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)
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 <[email protected]>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 <[email protected]>wrote:
>
>> On 13/09/2011 2:27 PM, [email protected] 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" <[email protected]> <[email protected]>
>> Date: Mon, 12 Sep 2011 22:35:28
>> To: <[email protected]> <[email protected]>; Discussion list
>> for GROMACS users<[email protected]> <[email protected]>
>> Reply-To: [email protected]
>> Subject: Re: [gmx-users] g_dist error
>>
>>
>> [email protected] 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" <[email protected]> <[email protected]>
>> Sender: [email protected]
>> Date: Mon, 12 Sep 2011 07:52:54
>> To: Discussion list for GROMACS users<[email protected]>
>> <[email protected]>
>> Reply-To: [email protected],
>> Discussion list for GROMACS users <[email protected]>
>> <[email protected]>
>> 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 <[email protected]
>> <mailto:[email protected]> <[email protected]>> 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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