[gmx-users] angle calculation

[Mila Miletić]

Great, thanks a lot!

2016-07-22 15:58 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 7/22/16 9:10 AM, Mila Miletić wrote:
>
>> Hello,
>>
>> I have recently tried to compute an angle between the COMs of three
>> specific groups,
>> so what I have done is:
>> 1. I used 'gmx gangle' program with a following command: gmx gangle -f
>> *.xtc -s  *.tpr -n index.ndx -g1 vector -group1 "com of group "g1" plus
>> com
>> of group "g2"" -g2 vector -group2 "com of group "g2" plus com of group
>> "g3"" -oav  "output.xvg".
>> 2. To check the obtained result, I also tried the other way: I got the COM
>> coordinates for three specific groups using 'gmx traj' program, then I
>> used
>> a written script to calculate the angle between the vectors that are
>> connecting these 'COM points'. So I was going with: if you have
>> coordinates
>> for three points A, B, C (your COMs), you need to find an angle formed by
>> A→
>> B→C. The script looked like this:
>>
>> paste group1_com.xvg group2_com.xvg >  group12_com.xvg
>> paste group2_com.xvg group3_com.xvg >  group23_com.xvg
>> awk '{ print $6-$2, $7-$3, $8-$4 }' group12_cm.xvg > AB.dat
>> awk '{ print $6-$2, $7-$3, $8-$4 }' group23_cm.xvg > BC.dat
>> paste AB.dat BC.dat > abbc_paste.dat
>> awk '{rez+=$1*$4 + $2*$5 + $3*$6; n++} END {print rez/n}' abbc_paste.dat >
>> AB_times_BC.dat
>> awk '{length1+=(sqrt($1*$1+$2*$2+$3*$3)); n++} END {print length1/n}'
>> AB.dat > AB_length.dat
>> awk '{length2+=(sqrt($1*$1+$2*$2+$3*$3)); n++} END {print length2/n}'
>> BC.dat > BC_length.dat
>> paste AB_length.dat BC_length.dat AB_times_BC.dat > angle_result.dat
>> awk '{ print $3/$1*$2}' angle_result.dat
>>
>> So in the first case I've got an angle about 8 degrees, and in other case
>> about 78 degrees. So I would also be grateful to hear some oppinion on
>> this.
>> The molecule in my case is p-Sexiphenyl at T=1K, so the first result for
>> smaller angle could be more probable to be correct in my case.
>> I am pretty new in this so this is just an idea how this issue may be
>> solved.
>>
>>
> Write the COM coordinates to a PDB file, load it in VMD, and have it
> calculate the angle.  If it checks out with your calculation, it's correct.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
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