Hello Bagherpour!
The rk1 ... rk4 correspond to the harmonic bias potential and the r1 ...r4
correspond to the restraint amount (distance or angle).
See page 122 of the Amber12 manual for a detailed explanation.
Hope this helps!
Rodrigo.
On Thu, Apr 19, 2012 at 8:13 AM, mehdi bagherpoor <ms.nightsky.gmail.com>wrote:
> Dear Amber user
>
> I am M.Bagherpour an M.Sc student of physics at Institute for Advanced
> Studies in Basic Science (www.iasbs.ac.ir).
>
> I am using Amber software for DNA simulation (Amber10). Specially in my
> project I need to exert external force in the end of DNA, The DNA that I
> want to simulate has 17 bp.
>
> Also what is the meaning of r1 & r2 & r3 & r4 & rk2 & rk3 in:
>
> &rst iat=39,40,42,43, r1=0., r2=170., r3=170., r4=360., rk2 = 30.,
> rk3 = 30.,
>
> I would appreciate your help.
> Looking forward to hearing from you.
>
> Best regards
> Mehdi
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Received on Thu Apr 19 2012 - 09:00:05 PDT
