[gmx-users] Gmx distance
Justin Lemkul
jalemkul at vt.edu
Sat Nov 3 17:25:43 CET 2018
On 11/2/18 11:36 AM, rose rahmani wrote:
> but this is output of -oall. its not a single value?!
You are asking in your command for all interatomic distances between the
groups (presumably, because you haven't shown your selection). This
command won't yield what you're hoping to see and my advice does not
apply for this type of situation (which doesn't seem to even match your
original statement of your problem).
> gmx distance -f md2.xtc -oall dist.xvg -n index.ndx
> # gmx distance is part of G R O M A C S:
> #
> #
> ¸<8d><9a><9a><91>ÃÂ<9a><9b>ð<8d><9e><91><98><9a>ò<9e><98><9a><91><8b><9e>þ<85><8a><8d><9a>ü<86><9e><91>ì<94><86><9d><99a>8a><<
> #
> @ title "Distance"
> @ xaxis label "Time (ps)"
> @ yaxis label "Distance (nm)"
> @TYPE xy
>
> 1.000 0.229 0.229 0.446 0.582 0.446 0.229 0.446
> 0.583 0.447 0.229 0.447 0.227 0.228 0.229 0.446
> 0.582 0.446 0.228 0.446 0.583 0.447 0.228 0.447
> 0.227 0.227 0.228 0.446 0.582 0.446 0.227 0.446
> 0.583 0.447 0.227 0.447 0.227 0.228 0.229 0.446
> 0.582 0.446 0.228 0.446 0.583 0.447 0.228 0.447
> 0.227 0.228 0.229 0.446 0.582 0.446 0.228 0.446
> 0.583 0.447 0.228 0.447 0.227 0.229 0.229 0.446
> 0.582 0.446 0.229 0.446 0.583 0.447 0.229 0.447
> 0.227 0.229 0.229 0.446 0.582 0.446 0.229 0.446
> 0.583 0.447 0.229 0.447 0.227 0.228 0.229 0.446
> 0.582 0.446 0.228 0.446 0.583 0.447 0.228 0.447
> 0.227 0.228 0.229 0.446 0.582 0.446 0.228 0.446
> 0.583 0.447 0.228 0.447 0.227 0.227 0.228 0.446
> 0.582 0.446 0.227 0.446 0.583 0.447 0.227 0.447
> 0.227 0.228 0.229 0.446 0.582 0.446 0.228 0.446
> 0.583 0.447 0.228 0.4
> .
> .
> .
>
> and this is -o of g_dist;
> g_dist -f md2.xtc -s md2.tpr -n index -o all.xvg
> #
> # g_dist is part of G R O M A C S:
> #
> # GRowing Old MAkes el Chrono Sweat
> #
> @ title "Distance"
> @ xaxis label "Time (ps)"
> @ yaxis label "Distance (nm)"
> @TYPE xy
> @ view 0.15, 0.15, 0.75, 0.85
> @ legend on
> @ legend box on
> @ legend loctype view
> @ legend 0.78, 0.8
> @ legend length 2
> @ s0 legend "|d|"
> @ s1 legend "d\sx\N"
> @ s2 legend "d\sy\N"
> @ s3 legend "d\sz\N"
> 0.0000000 0.2176011 -0.0120678 -0.0465498 0.2122209
> 1.0000000 0.2124534 -0.0301750 -0.0463870 0.2051198
> 2.0000000 0.1923753 -0.0158403 -0.0510135 0.1848106
> 3.0000000 0.1885315 -0.0107298 -0.0488160 0.1817856
> 4.0000000 0.2044982 -0.0052650 -0.0490329 0.1984630
> 5.0000000 0.2033602 -0.0002742 -0.0429537 0.1987720
> 6.0000000 0.2050487 0.0013833 -0.0444658 0.2001646
> 7.0000000 0.2002475 0.0041072 -0.0415003 0.1958568
> 8.0000000 0.2006473 0.0033450 -0.0511889 0.1939790
> 9.0000000 0.2032918 -0.0000119 -0.0330052 0.2005947
> 10.0000000 0.2255659 0.0003929 -0.0415857 0.2216990
> 11.0000000 0.2243811 0.0118313 -0.0344751 0.2214010
> 12.0000000 0.2347855 0.0078275 -0.0383532 0.2314994
> 13.0000000 0.2371541 0.0081918 -0.0388267 0.2338107
Here, you have what you want (I assume), and the first column after the
time is all you need. It's the distance, which also can't be negative
because it is the magnitude of the vector length and is unsigned.
-Justin
> .
> .
> .
>
>
> On Thu, Nov 1, 2018 at 11:39 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 11/1/18 2:25 PM, rose rahmani wrote:
>>> I don't know how? I mean x,y,z(s1, s2,s3) in dist.xvg can easily be
>>> multiplied by (-), but how should i modify second column,i don't know how
>>> s0 is calculated by g_distance to modify it??
>> The output of -oall is a single value, the actual distance, which I
>> assume is what you are talking about in your previous message. You can
>> parse that column in any scripting language you like and
>>
>> [ pseudocode, not functional ]
>> if (value < 0)
>> {
>> value *= -1
>> }
>>
>> -Justin
>>> On Wed, 31 Oct 2018, 19:38 Justin Lemkul, <jalemkul at vt.edu> wrote:
>>>
>>>> On 10/31/18 12:06 PM, rose rahmani wrote:
>>>>> Hi,
>>>>>
>>>>> I want to calculate distances between fixed tube in the middle of the
>> box
>>>>> and amino acids(all are same type)around it. But gmx distance gives me
>>>> the
>>>>> relative distance i mean AA can be front or back( can be 0.5 or -0.5
>> from
>>>>> tube) of tube but still |-0.5|=0.5 nm far from it. How can i have the
>>>>> absolute value of distances?
>>>>> Would you please help me?
>>>> Write a simple post-processing script that multiplies any negative value
>>>> by -1.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Virginia Tech Department of Biochemistry
>>>>
>>>> 303 Engel Hall
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.thelemkullab.com
>>>>
>>>> ==================================================
>>>>
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>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
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