[gmx-users] Gmx distance
jalemkul at vt.edu
Thu Nov 1 21:09:26 CET 2018
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
> On Wed, 31 Oct 2018, 19:38 Justin Lemkul, <jalemkul at vt.edu> wrote:
>> On 10/31/18 12:06 PM, rose rahmani wrote:
>>> 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
>>> 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 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
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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