Re: [AMBER] rror: an illegal memory access was encountered launching kernel kNLSkinTest

From: David Case <>
Date: Sat, 18 Jan 2020 13:31:36 +0000

On Sat, Jan 18, 2020, Sruthi Sudhakar wrote:

>I tried including the
>vlimit in the input script but still the error repeated.

You have atoms in your starting structure that are almost on top of one
another. Use the "check" commands in cpptraj or parmed to tell you
which ones they are. You will need to fix this before proceeding.

Second: you should generally plan to do a minimization first before
running MD.

Third: when problems occur, use the CPU version of pmemd, set ntpr=1 and
nstlim to 100 (or so): this will provide more useful diagnostic


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Received on Sat Jan 18 2020 - 06:00:02 PST
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