[gmx-users] Gmx distance

[Justin Lemkul]

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

==================================================