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From: Daniel Roe <daniel.r.roe.gmail.com>

Date: Wed, 1 Dec 2021 08:20:15 -0500

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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*

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*

*>
*

*> |
*

*>
*

*>
*

*>
*

*> | |
*

*>
*

*> 本邮件及其附件含有发送给特定个人和用于特定目的的信息。如果您不是预期的收件人，请立即删除本邮件并通知发件人。严禁任何非预期的收件人使用、传播、分发或复制本邮件或其附件。
*

*> This email and its attachments may contain confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this email and notify the sender immediately. Any use, dissemination, distribution, or copying of this email or its attachments by persons other than the intended recipient(s), is strictly prohibited.
*

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Received on Wed Dec 01 2021 - 05:30:02 PST

Date: Wed, 1 Dec 2021 08:20:15 -0500

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:

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Received on Wed Dec 01 2021 - 05:30:02 PST

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