Re: [AMBER] Kinetic Energy is zero in production run.

From: Matias Machado <>
Date: Sat, 27 Jul 2019 18:13:18 -0300 (UYT)

Dear Amit Kumar,

I don't see the need for using "nmropt=1" if you are setting the same temperature along the whole simulation... anyway, you may be missing the definition of the temperature value within the session TYPE='TEMP0', so probably you were running at 0 K, that is something you can easily check... Hence if you insist on using this session, then the proper way to set it is:

 &wt TYPE='TEMP0',
  istep1 = 0, istep2 = 2500000,
  value1 = 298.0, value2 = 298.0,
 &wt TYPE='END' /



Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "Amit Kumar" <>
Enviados: Sábado, 27 de Julio 2019 8:38:18
Asunto: [AMBER] Kinetic Energy is zero in production run.

Dear Amber users,
I ran a simulation of alpha-synuclein fiber for 5ns (with and without
torsional restraint) using Amber16. I used implicit solvent (igb=5) and
after 5ns of short simulation (each with and without restraint) I analysed
the results in terms of RMSD and structural Persistence order parameter.
There I met a bizarre as, both P(Structural persistence order parameter)
and RMSD (for unrestrained one) reached a plateau after a few picoseconds
run, and when it is visualised on vmd I saw that just after loading and
starting vibration it stopped vibrating. In out file, the value of Kinetic
Energy was zero while for the restrained simulation the result was fine
means showing some trend.
Can anyone explain it? why did this happen? The RMSD graph (for
unrestrained simulation) is also attached.
#Script for unrestrained simulation.
   ntp = 0, ntwx=100, nstlim=2500000,
   dt=0.002, ntt=3,
   temp0=298, gamma_ln=1.0, ig=-1,
   ntc=2, ntf=2, cut=999, rgbmax = 30.0,
   ntb=0, igb=5, ioutfm=1, nmropt=1,
   TYPE='TEMP0', ISTEP1=1, ISTEP2=2500000,
 &wt TYPE='END' /

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