we also have trouble with adding caps to 1UBQ since there seems to be a
steric clash at the start. Other systems with caps added seem to work fine
for us with ff19SB up to hundreds of ns on the CUDA version. Maybe you can
send us offlist your prmtop, inpcrd and mdin files for the one that doesn't
work? maybe the mdout as well so we can compare energies etc. If you can
send the original mdout that crashes, and also run a short run of 100 steps
with ntpr=1 so we can see if we reproduce the energies and forces from your
setup.
carlos
On Tue, Dec 17, 2019 at 9:22 AM Pavlína Pokorná <pokorna.pavlina.ibp.cz>
wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Dec 17 2019 - 08:30:03 PST
