Hi,
I think I understand what's going on here. The 'range360' keyword for
'multidihedral' (as you probably know) just adds 180 to the original
torsion (which ranges from -180 to 180). However, when the average is
calculated by the 'phipsi' analysis, the following formula is used
(since it easily incorporates periodicity):
AvgTorsion = ArcTangent( SUM[sin(theta)], SUM[cos(theta)] )
The range of the ArcTangent() function is -180 to 180, so no matter
what the original values are, that's the range of the values after
averaging. I suppose I could add a 'range360' keyword to the 'phipsi'
analysis. If you think that would be useful add the issue here:
https://github.com/Amber-MD/cpptraj/issues.
In the meantime, you could convert the values from 'phipsi' manually
if you want (i.e. if theta > 180 subtract -180, if theta < 0 add 180).
Hope this helps,
-Dan
On Wed, Dec 1, 2021 at 5:04 AM 余青芬 <yuqf5.mail.sysu.edu.cn> wrote:
>
> Dear Amber20,
>
>
>
>
> I used Amber20 phipsi to calculate the avg and std for dataset DPDP with range360 on Ubuntu20.
>
>
>
>
> The avgs are negative. With "range360" are they supposed to be positive?
>
>
>
>
> Here is the process:
>
> parm mydata_sol_cmap.top
> trajin mydata_sol_cmap_1C.md.crd
> strip :WAT
> strip :Na+
> strip :Cl-
> multidihedral DPDP phi psi range360 out mydata_multi.dat
> run
> phipsi DPDP[phi] DPDP[psi] out mydata_phipsi.dat resrange 2-2
>
>
>
>
> Outputs:
>
> #mydata_multi.dat
>
> #Frame psi:1 phi:2 psi:2 ...
>
> 1 148.3643 246.5573 4.0019 ...
> ...
>
> 20000 165.2981 276.8591 358.8114 ...
>
>
>
>
> #mydata_phipsi.dat
>
> #Phi Psi SD(Phi) SD(Psi) Legend
> -105.2002 -21.5605 43.5147 67.0081 "phi:2-psi:2"
>
>
>
>
> Thank you.
>
>
>
>
> Best,
>
>
>
>
> Qingfen
>
>
>
>
>
>
>
>
>
>
>
>
>
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Received on Wed Dec 01 2021 - 05:30:02 PST
