yes, it was with SHAKE. Thanks for your effort.
On Tue, Dec 17, 2019 at 3:02 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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
> > >> >
> > >> _______________________________________________
> > >> 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
> > >
> >
> >
> > --
> > *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
>
--
*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 Tue Dec 17 2019 - 06:30:03 PST
