On Thu, Aug 14, 2025, Beierlein, Frank via AMBER wrote:
>
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
> Etot = -106290.2119 EKtot = 0.0000 EPtot = -106290.2119
> BOND = 10916.9779 ANGLE = 122.0025 DIHED = 403.4883
> 1-4 NB = 153.0514 1-4 EEL = -3075.5267 VDWAALS = 20127.5335
> EELEC = -134937.7969 EHBOND = 0.0000 RESTRAINT = 0.0582
> EAMBER (non-restraint) = -106290.2700
> DV/DL = 139.0082
Note the the bond energy is very high at step 0. Use the "checkstructure"
action in cpptraj to print out suspicious bonds.
It's worth turning off TI for a short simulation (say nstlim=25, ntpr=1) to
see if the problem is really related to TI. Even if it is related to TI,
don't set ntpr to some large value like 10000: you need to figure out what
is going on right at the beginning of your simulation.
...hope this helps...dac
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Received on Fri Aug 15 2025 - 07:00:02 PDT
