I am sorry for missing a zero, it has about 2000 atoms. The nonUnit cell
dimensions shown in leap are below:
Scaling up box by a factor of 1.388963 to meet diagonal cut criterion
Solute vdw bounding box: 6.972 12.236 13.693
Total bounding box for atom centers: 35.916 35.916 35.916
(box expansion for 'iso' is 28.2%)
Solvent unit box: 18.774 18.774 18.774
Volume: 25155.321 A^3 (oct)
I am also putting my input file, in case I am doing something
inappropriate:
-----------------------------------
&cntrl
imin=0,
nstlim=50000000,
dt=0.002,
irest=1,
ntx=5,
iwrap=0,
ntpr=10000,
ntwx=10000,
ntwr=10000,
ioutfm=1,
ntf=1,
ntb=2,
cut=10.0,
temp0=300.0,
ntt=3,
gamma_ln=2.0,
ntp=1,
pres0=1.0,
taup=1.2,
ntc=2,
&end
------------------------------------------------------
What I wonder most is why MD keeps running despite having NAN in energy
terms and coordinates.
Thanks,
Mish
On Wed, Nov 3, 2021 at 2:15 PM David A Case <david.case.rutgers.edu> wrote:
> On Wed, Nov 03, 2021, mish wrote:
> >
> >I am running a simulation of a small system (~200 atoms) at NPT using
> Amber
> >20 and RTX2080 cards.
>
> What is your unit cell size? Your nonbonded cutoff? I'm surprised that
> you
> can even run a system with only 200 atoms in Amber. It may be that you are
> hitting a lower limit (after more than 100 ns!) that the code can't handle.
>
> ....dac
>
>
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Received on Wed Nov 03 2021 - 14:00:02 PDT
