[gmx-users] g_dist error

[Mark Abraham]

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>
> Date: Mon, 12 Sep 2011 22:35:28
> To:<aiswarya.pawar at gmail.com>; Discussion list for GROMACS users<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>
>> 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>
>> Reply-To: jalemkul at vt.edu,
>> 	Discussion list for GROMACS users<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>>  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>  | (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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