Dear Carlos,
thanks for your reply, I was not aware of this. I use equilibration
protocols with gradual heating and decrement of heavy-atom restraints
followed by a 1 ns of unbiased simulation run before starting cuda
simulations. So I guess the structure should be well-equilibrated. Still, I
can try to modify my setup to give the system more time to equilibrate.
Regards,
Pavlina
On Wed, Dec 11, 2019 at 12:57 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> We haven't seen problems with standard caps - they actually use ff14SB so
> should not be a problem. There are times when a poor quality structure may
> just be ok with Cuda for ff19SB but not ff14SB (or vice versa) - is this
> for a well equilibrated system?
>
> On Wed, Dec 11, 2019, 5:38 AM Pavlína Pokorná <pokorna.pavlina.ibp.cz>
> wrote:
>
> > Dear all,
> >
> > when attempting simulations with ff19SB with the updated Amber18 version
> > from Carlos Simmerling's GitHub, I failed to run pmemd.cuda simulations
> > with ACE and NHE caps on N- and C- termini of the protein. Simulations
> > crashed with the following error in ~50 nanoseconds: "Error: an illegal
> > memory access was encountered launching kernel kNLSkinTest". No further
> > error message is printed in the simulation *.out file and the last-saved
> > structure showed no abnormalities. Simulations with the same system
> without
> > the end-caps run without any problems. Runs with the end-caps with sander
> > on CPUs do not result in this error. Test ff14SB cuda simulations with
> the
> > end-caps with the updated Amber18 run also without problems. I have ~1100
> > atoms in my system.
> >
> > It seems that cuda + ff19SB + caps combination produces some large
> numbers
> > somewhere. Is there something I am missing or could you advise any
> possible
> > solution to my problem?
> >
> > The ff19SB improved some local backbone conformations (and associated
> > protein-protein interactions) wrt ff14SB in my protein-protein complex,
> so
> > I'd like to use this force field. Still, I need to use the end-caps due
> to
> > the excessive and undesired end-end interactions in the structure.
> >
> > I'd be grateful for any comment.
> >
> > Best wishes,
> > Pavlina
> >
> > --
> > Pavlina Pokorna
> > *PhD student*
> > Institute of Biophysics of the CAS, v. v. i.
> > Kralovopolska 135, 612 65 Brno
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
*Mgr. Pavlína Pokorná*
*PhD student*
Institute of Biophysics of the CAS, v. v. i.
Kralovopolska 135, 612 65 Brno
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Received on Wed Dec 11 2019 - 06:00:03 PST
