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,
&cntrl
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,
&end
END
END
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
here?
I usually do the minimization and equilibrations too again and then do the
production run and hence have never experienced such exact similarity.
Thanks
Suchetana
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 17 2023 - 14:00:02 PST
