Date: Sat, 27 Jul 2019 17:08:18 +0530
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.
prod_run1
&cntrl
imin=0,
irest=1,
ntx=5,
ntpr=2000,
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,
/
&wt
TYPE='TEMP0', ISTEP1=1, ISTEP2=2500000,
/
&wt TYPE='END' /
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(image/png attachment: unrestrained_rmsd.png)
