[gmx-users] Distance between COM of two groups

[Sajjad Kavyani]

Thanks for the reply Justin,
Actually the pulling process is so simple where the group1 is fixed in one
side of the box and the group2 on the other side (box center is in the
middle). And the group2 is moving toward group1 (in a straight z
direction). It is so logical that the distance between them must start from
a maximum value  and decreases over time but the output distance from "gmx
distance" is a growing value and after some times it decrease slightly!! I
checked the trajectory with vmd and it shows what I was expected and the
group2 approach over time to group1 and the distance decreases. It seems
that everything is correct except the "gmx distance" output.

Actually it seems that the thing that one of the groups is in the negative
side of the box vector (consider group2 at z = -a and group1 at z = +b),
the gmx distance tool subtract the "a" from "b" until it passes the zero
point in the middle of the box and after that the distance decreases vs.
time!!!

Please find the "gmx distance" output in the attachment.

Cheers

On Sun, Jun 19, 2016 at 3:22 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 6/18/16 9:40 AM, Sajjad Kavyani wrote:
>
>> Dear experts,
>>
>> I am puling group2 toward group1 and I want to calculate the distance
>> between COM of two groups versus time.
>> For the g_dist it was a straightforward process with the selection menu.
>> But for the "gmx distance" I used:
>>
>> gmx distance  -f test.xtc -s test.tpr -oav -oxyz -n index.ndx
>> -select 'com of group "group1" plus com of group "group2"'
>>
>> But both outputs distances are a growing value over time (!!)
>> (actually the average value is the same with sqrt(x^2+y^2+z^2)) where
>> the distance meant to be decrease over time!
>>
>> Could you please help me with the commands?
>>
>>
> That's the correct command.  Is there some reason why you think the result
> is wrong?  Are your group definitions correct for the analysis you're
> trying to perform?
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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