On Mon, Jan 28, 2019, Debarati DasGupta wrote:
>
>
>I am sending all the required input file to generate the error I got.
>It seems to happen for 2 systems (acetonitrile single molecule in water (TIP3P) and isopropanol in water TIP3P)
>
>sander -O -i min_all.in -o allmin.out -p C3N_WAT.prmtop -c C3N_WAT.inpcrd
>-r allmin.rst -x allmin.crd -ref C3N_WAT.inpcrd
>
>
>sander -O -i min_all.in -o allmin.out -p IPA_WAT_box.prmtop -c
>IPA_WAT_box.inpcrd -r allmin.rst -x allmin.crd -ref IPA_WAT_box.inpcrd
I see the segfault for the second case, but not the first. I think this
is related to the need to have SHAKE on for TIP3P (and other rigid)
water molecules.
Try adding ntc=2 to your input files. You won't be able to minimize to
a complete minimum, but your states should be fine for subsequent MD.
...good luck...dac
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Received on Tue Jan 29 2019 - 18:30:02 PST
