What is the initial model? Is it an experimental structure?
On Wed, Dec 11, 2019, 8:35 AM Pavlína Pokorná <pokorna.pavlina.ibp.cz>
wrote:
> 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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>
>
> --
> *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 - 06:30:02 PST
