Re: [AMBER] Calculation of dihedral angle using cpptraj in CpHMD simulation

From: Carlos Simmerling via AMBER <>
Date: Thu, 1 Sep 2022 09:45:32 -0400

Remember that a dihedral is a circular value but you're plotting it on a
linear scale. Use dots because lines imply a direction of the transition,
and in general you don't know which way it rotated. I'm your plot I would
guess that it went from top to bottom withiut going across the middle.

On Thu, Sep 1, 2022, 9:31 AM Dulal Mondal via AMBER <>

> Dear Users,
> I am running a CpHMD simulation in explicit solvent. I am interested
> in calculating an important dihedral angle. Upon the calculation of the
> dihedral angle over time, I have seen too many fluctuations which look
> absurd to us. In the attached figure you can see that there are some peaks
> which travel from +180 to -180 in no time. I am also attaching the input
> for the production run herewith.
> Production
> &cntrl
> imin=0, ntx=5, irest=1,
> iwrap=1, nstlim=10000000,
> dt=0.001, temp0=300.0,
> ntpr=5000, ntwx=5000,
> cut=10.0, ntb=1, ntp=0,
> ntt=3, gamma_ln=2.0,
> icnstph=2, solvph=8.0,
> ntcnstph=500, ntrelax=200,
> saltcon=0.1, ig=-1,
> /
> Is ttis input correct for the production run of CpHMD in explicit solvent?
> If there is any change please let me know. Any help will be appreciated.
> With regards,
> Dulal Mondal
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Received on Thu Sep 01 2022 - 07:00:48 PDT
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