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

From: Dulal Mondal via AMBER <amber.ambermd.org>
Date: Thu, 1 Sep 2022 19:01:14 +0530

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.

  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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(image/png attachment: cpptraj_dihedral_his64.png)

Received on Thu Sep 01 2022 - 07:00:24 PDT
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