On Sat, Mar 25, 2017, Sadegh Faramarzi Ganjabad wrote:
>
> I am running simulations with AMBER using CHARMM ff. The first simulation
> goes well, but when I restart it, the structure looks abnormal with
> extraordinarily long bonds and no water box. And here is what I see in my
> output file;
>
> NSTEP = 50000 TIME(PS) = 20050.000 TEMP(K) =********* PRESS =
> 34350.4
> Etot = ************** EKtot = ************** EPtot =
Something is clearly wrong, but we don't have enough information to offer
much help. It's not clear whether the fact that you are using the CHARMM
force field is relevant.
You will need to examine (and report here if you can't figure this out),
how you saved the restart file, and how to started the restart calculation.
How did you determine that the second simulation had "no water box"?
The first goal is to look at the *start* of the second simulation, not the
end. Do the energies at the first steps of the second simulation match those
at the end of the first one?
The simplest explanation is that something bad happened during the second
simulation. Finding such problems can be difficult: you'll need to explore
some, along the lines outlined above, to narrow down the problem.
....dac
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Received on Tue Mar 28 2017 - 10:00:02 PDT
