Re: [AMBER] knlskintest error when using HMR with 4fs

From: David A Case <>
Date: Mon, 7 Jun 2021 14:47:40 -0400

On Mon, Jun 07, 2021, Neville Bethel wrote:
>If I use a 4 fs time step for production, my simulations crash within a few
>nanoseconds, if I restart these simulations they will run for a few
>nanoseconds before crashing again.

Thanks for the report: a few questions:

1. Is there a reason you put "knlskintest error" in your subject line? Did
you get any kind of error message?

2. What version of Amber are you using? Are you running pmemd.cuda? Are
there non-protein components in your simulation?

3. It's worth double-checking that your prmtop file is indeed the one
that has the repartioned masses. (This may sound trivial, but I've made the
mistake myself of using the original rather than the modified prmtop....)

4. A long shot here, and you might want to wait for others to reply:
consider, as a test, rebuilding your system with ff14SB rather tha ff19SB.
You should not need to re-equilibrate: just see if using the ff14SB prmtop
file (with HMassRepartition) gives different behavior. Since it only takes
a few nanoseconds to fail, this should not be all that much work. There is
anecdotal information that something in ff19SB [CMAP ??] might become
unstable in certain circumstances.

5. Again, since you seem to get failures quickly, try some tweaks to the
input file: (a) set iwrap=0; (b) set ntb=1 and ntp=0. These are just
tests to possible help narrow down the range of problems.


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Received on Mon Jun 07 2021 - 12:00:03 PDT
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