we're testing things on our end to try to reproduce the problem. just to
clarify, you also used shake with the 4fs and HMR, right?
On Mon, Dec 16, 2019 at 4:59 AM Pavlína Pokorná <pokorna.pavlina.ibp.cz>
wrote:
> Dear Carlos,
>
> I have started cuda simulation from ~150 ns restart from my sander run,
> simulation crashed after again in about the same time as in previous tests.
> I further tested the same thing (ff19SB with and without end-caps) on 1UBQ
> structure without any further modifications to test whether there possibly
> was a problem in the starting structures of my two previous systems. (I
> chose 1UBQ based on ff19SB paper.) With proper equilibration again. And I
> arrived at the same problem again... simulation without caps runs but the
> one with caps crashed in about 14 ns.
>
> I'm running all my simulations with hydrogen mass repartitioning (dt =
> 0.004). I run also a test 1UBQ simulation with end-caps without HMR (but
> with SHAKE, dt = 0.002). This simulation runs with no problems. The larger
> time step might be where the forces are getting too large... You said You
> hadn't seen problems with standard caps - was it in simulations without
> HMR?
>
> Kind regards,
> Pavlina
>
>
> On Wed, Dec 11, 2019 at 6:07 PM Pavlína Pokorná <pokorna.pavlina.ibp.cz>
> wrote:
>
> > it was reproducible in several simulations of the two systems I tested.
> > Many thanks for your ideas, I’ll try them and let you know the results.
> >
> >
> >
> > On Wed, 11 Dec 2019 at 17:55, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> >> I still think it's worth trying to simulate what is in the crystal. Or
> >> maybe take your restart from longer md in ff14SB and switch to ff19SB.
> >> GPUs
> >> can be finicky with high energies from poor initial models. Not sure why
> >> capped vs not matters - that shouldn't change any usage of ff19SB. Is he
> >> problem reproducible in capped vs uncapped? Just trying to think of
> >> explanations...
> >>
> >> On Wed, Dec 11, 2019, 11:51 AM Pavlína Pokorná <pokorna.pavlina.ibp.cz>
> >> wrote:
> >>
> >> > I don’t think this is the problem as the same structure without
> end-caps
> >> > runs OK. I also had the same issue with second system I tested
> (another
> >> > protein, a bit lower resolution), which didn’t contain any other
> >> > modifications wrt crystal structure than the end-caps...
> >> >
> >> > On Wed, 11 Dec 2019 at 16:08, Carlos Simmerling <
> >> > carlos.simmerling.gmail.com>
> >> > wrote:
> >> >
> >> > > maybe you can try first without the mutations, so you know that the
> >> > initial
> >> > > model is good?
> >> > >
> >> > > On Wed, Dec 11, 2019 at 9:40 AM Pavlína Pokorná <
> >> pokorna.pavlina.ibp.cz>
> >> > > wrote:
> >> > >
> >> > > > yes, it is based on X-ray structure with 1.8A resolution but few
> >> > > > solvent-exposed residues are mutated.
> >> > > >
> >> > > >
> >> > > > On Wed, Dec 11, 2019 at 3:04 PM Carlos Simmerling <
> >> > > > carlos.simmerling.gmail.com> wrote:
> >> > > >
> >> > > > > 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
> >> > > > > > > > _______________________________________________
> >> > > > > > > > AMBER mailing list
> >> > > > > > > > AMBER.ambermd.org
> >> > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > > > > > > >
> >> > > > > > > _______________________________________________
> >> > > > > > > AMBER mailing list
> >> > > > > > > AMBER.ambermd.org
> >> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > > > > > >
> >> > > > > >
> >> > > > > >
> >> > > > > > --
> >> > > > > > *Mgr. Pavlína Pokorná*
> >> > > > > > *PhD student*
> >> > > > > > Institute of Biophysics of the CAS, v. v. i.
> >> > > > > > Kralovopolska 135, 612 65 Brno
> >> > > > > > _______________________________________________
> >> > > > > > AMBER mailing list
> >> > > > > > AMBER.ambermd.org
> >> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > > > > >
> >> > > > > _______________________________________________
> >> > > > > AMBER mailing list
> >> > > > > AMBER.ambermd.org
> >> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > > > >
> >> > > >
> >> > > >
> >> > > > --
> >> > > > *PhD student*
> >> > > > Institute of Biophysics of the CAS, v. v. i.
> >> > > > Kralovopolska 135, 612 65 Brno
> >> > > > _______________________________________________
> >> > > > AMBER mailing list
> >> > > > AMBER.ambermd.org
> >> > > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > > >
> >> > > _______________________________________________
> >> > > AMBER mailing list
> >> > > AMBER.ambermd.org
> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> > >
> >> > --
> >> > *PhD student*
> >> > Institute of Biophysics of the CAS, v. v. i.
> >> > Kralovopolska 135, 612 65 Brno
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > 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
> >
>
>
> --
> *Mgr. Pavlína Pokorná*
> *PhD student*
> Institute of Biophysics of the CAS, v. v. i.
> Kralovopolska 135, 612 65 Brno
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Dec 17 2019 - 06:30:02 PST
