Re: [AMBER] simple minimization error of a acetonitrile molecule in water (TIP3P water)

From: David Case <>
Date: Wed, 30 Jan 2019 02:10:52 +0000

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 -o allmin.out -p C3N_WAT.prmtop -c C3N_WAT.inpcrd
>-r allmin.rst -x allmin.crd -ref C3N_WAT.inpcrd
>sander -O -i -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
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