On Sat, Aug 02, 2025, Sudipti Priyadarsinee via AMBER wrote:
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
>0.0
> 1-4 NB = 419.7488 1-4 EEL = 3333.8362 VDWAALS =
>**************
1-4 NB = 419.7488 1-4 EEL = 3333.8362 VDWAALS =
**************
EELEC = -155305.2758 EHBOND = 0.0000 RESTRAINT =
2.1654
This indicates that your van der Waals term is very high, even the on the
first step. MD will never work with such a bad initial structure.
Use the "checkstructure" action in cpptraj to identify bad contacts, and try
to see if you can fix them. Since your EEL energy is not incredibly high,
it could be that some initial minimization would help: try doing 25 (say)
steps of minimization in sander using ntmin=3. (Set ntpr=1 to get the most
detailed information about what is going on.)
Note that the Restraint energy is only 2 kcal/mol, which indicates that the
problems you are seeing have nothing to do with your restraints. You almost
certainly need to equilibrate your systems via minimization and careful
initial MD, before trying umbrella sampling.
...good luck...dac
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Received on Sat Aug 02 2025 - 14:30:03 PDT
