Hello,
Encountered error: „ERROR: Calculation halted. Periodic box dimensions have changed too much from their initial values.
Your system density has likely changed by a large amount, probably from
starting the simulation from a structure a long way from equilibrium."
I run my simulations in 10 x 10 ns jobs using GPU. They keep failing at various stages, not just at the first interval—one job even terminated in the 9th interval! Although the errors suggest this might be due to significant density fluctuations, the density remains within the range of 1.0355 to 1.0383. I inspected the MD trajectory and didn’t notice any specific issues.
I use H-mass repartitioned topology generated with CPPTRAJ.
My input is:
production
&cntrl
imin=0,
ntx=5,
ntpr=1000,
ntwr=1000,
ntwx=1000,
ntwe=1000,
nscm=1000,
ntf=2,
ntc=2,
ntb=2,
ntp=1,
tautp=5.0,
taup=5.0,
nstlim=2500000,
t=0.0,
dt=0.004,
cut=9.0,
ntt=3,
gamma_ln=2.0,
ig=-1,
irest=1,
iwrap=1,
ioutfm=1,
&end
&ewald
ew_type = 0,
skinnb = 1.0,
&end
–
Maciej Spiegel, MPharm PhD
assistant professor
.GitHub <
https://farmaceut.github.io/>
Department of Organic Chemistry and Pharmaceutical Technology,
Faculty of Pharmacy, Wroclaw Medical University
Borowska 211A, 50-556 Wroclaw, Poland
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Received on Fri Nov 08 2024 - 01:00:02 PST
