> If you are talking about the entire system (protein + DNA) rotating: that is
> unlikely to be of much interest (aside from its use in estimating rotational
> diffusion.) Even a non-dissociating system will rotate (and translate)
> during MD.
No, I am talking about protein only ( after dissociation) in some trials it is rotated relative to initial coordinates while most of the trials the protein not rotate. So we think quantifying this rotation would be better to describe those trails (rotated ons)
Thanks, I will check the savematrices option
Best regards,
Mohamed Marzouk Sobeh
Ph.D student at Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
T.A Physics department,Ain Shams University, Cairo, Egypt.
Emails:
mohamed_marzouk.sci.asu.edu.eg
marzouk.aa.m.titech.ac.jp
marzouk_biophysics.yahoo.com
mohamedmarzoukphysics.gmail.com
Mob. and WhatsApp.:
+81 070-4070-9549
+2 01061417414
> On Oct 10, 2021, at 9:29 PM, David A Case <david.case.rutgers.edu> wrote:
>
> On Sun, Oct 10, 2021, mohamed marzouk wrote:
>
>> During my dissociation simulation for protein/DNA complex the system rotate
>> (noticed during visual inspection), So I want to quantify this rotation.
>
> If you are talking about the entire system (protein + DNA) rotating: that is
> unlikely to be of much interest (aside from its use in estimating rotational
> diffusion.) Even a non-dissociating system will rotate (and translate)
> during MD.
>
>> - How can I get the rotation matrix by CPPTRAJ from the reactive trajectory ?
>
> Use the savematrices option in the rmsd command.
>
> ....dac
>
>
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Received on Sun Oct 10 2021 - 06:00:02 PDT
