[AMBER] Multiple copies of simulation to check for reproducibility and convergence

From: Suchetana Gupta via AMBER <amber.ambermd.org>
Date: Tue, 17 Jan 2023 13:37:16 -0800

Dear Amber Users
I ran multiple copies of production run for a protein using the following
input file to check for the reproducibility and convergence:

md, npt, equilibrium to 300K quickly,
  imin = 0, ntx = 7, irest = 1,
  ntpr = 1000, ntwx = 1000, ntwe = 0, ntwprt=0,
  ntc = 2, ntf = 2, iwrap = 1, ioutfm = 1,
  nstlim = 5000000, dt =0.002,
  tempi=300.0, temp0 = 300.0, ntt =1, tautp =2.0,
  ntb = 2, ntp = 1, taup = 2.0, pres0 =1.0, cut = 9.0,

The commands that I used is :
pmemd.cuda -O -i md.in -p file.top -c eq.rst -o 1md.out -inf 1md.info -x
1md.crd -r 1md.rst
pmemd.cuda -O -i md.in -p file.top -c 1md.rst -o 2md.out -inf 2md.info -x
2md.crd -r 2md.rst

I used the same eq.rst for all the runs.

When I checked the output files (1md.out, 2md.out), I note identical values
of energy terms, despite the random seed being different (I made sure it
was different). The RMSD plots were also identical.

I wanted to know if so much identity is correct or am I missing something

I usually do the minimization and equilibrations too again and then do the
production run and hence have never experienced such exact similarity.

AMBER mailing list
Received on Tue Jan 17 2023 - 14:00:02 PST
Custom Search