have you seen the post I made earlier about ff19SB errors? I am not sure of
the exact issue, but each time I have checked someone's inputs it has
turned out that the structure has high energy contacts and worked fine with
careful equilibration. Can you tell us how you obtained the structure, and
if any parts needed to be modeled? Also your equilibration protocol may be
important so it can help to summarize that.
As Dave suggested, a small example is helpful, particularly if it doesn't
include unusual force field parameters or heavy atoms that needed to be
modeled.
On Fri, Nov 20, 2020 at 4:18 PM Liao <liaojunzhuo.aliyun.com> wrote:
> Continuing on this old thread, using vlimit=10 resolved the issue mostly,
> but there was still a 2% chance the simulation will crash within 5 ns.
>
> Now, working on a new protein-ligand system, I started out with ff14SB,
> runs normally as expected (Implicit water, HMR prmtop files used). When I
> decided to try ff19SB also, the simulation blows up again quite quickly.
> This time it doesn't give an error and stop, but the energy values have
> suddenly blown up. As mentioned last time by Dr Case, here I've provided my
> input files, including mol2 and PDB, preparation scripts and a short
> output. Maybe someone can rerun on their system, to see what their result
> is, and what modifications can be made? From another recent thread (
> http://archive.ambermd.org/202011/0181.html), Dr Simmerling mentioned
> that a slow 9-step equilibration protocol solved such issue. Don't know if
> that may be the ultimate solution to all?
>
>
> ------------------------------------------------------------------
> Sender:David A Case <david.case.rutgers.edu>
> Sent At:2020 Oct. 15 (Thu.) 07:17
> Recipient:Liao <liaojunzhuo.aliyun.com>; AMBER Mailing List <
> amber.ambermd.org>
> Subject:Re: [AMBER] vlimit=10 compromise for Amber 20 error: "an illegal
> memory access was encountered launching kernel kClearForces"?
>
> On Wed, Oct 14, 2020, Liao wrote:
> >
> >The 1st way is when I switch back to ff14SB (with nothing else changed
> >but the random seed), by regenerating the prmtop file, it runs and
> >completes normally. But since I’ve got Amber 20, I still want to try
> >use the ff19sb.
>
> Can you create a (small?) example that illustrates the problem with
> ff19sb? We would need a prmtop, inpcrd and mdin files, plus the actual
> command line you used to run the program.
>
> ...thanks...dac
>
>
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Received on Fri Nov 20 2020 - 15:00:02 PST
