On Mon, May 14, 2018, David Adrian Saez San Martin wrote:
>
> when I switch from sander.MPI (where everything goes fine) to
> pmemd.cuda.MPI or pmem.cuda, the simulation does not work. It says:
>
> Exiting due to the presence of inconsistent SHAKEH hydrogen clusters,
> > Hi, I think I am having with Amber2017 the same problem posted here:
> >
> > archive.ambermd.org/201209/0247.html
> >
> > Just want to know if there exists a solution. I created my topology
> > with parmed/chamber and it works perfectly with sander, but when I apply
> > ntc=1 the multiple bond error makes reference to a non-hydrogen atom.
The archive doesn't make it clear (at least to me) whether pmemd is
making an error (I think that is less likely), or that the prmtop file
coming from a psf via parmed/chamber is broken (which I think is rather
more likely). But I don't know that any developer has a example that
fails in this way: can you post a smallish example (or largish, if that
is all you can come up with)?
...thanks....dac
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Received on Tue May 15 2018 - 13:30:03 PDT
