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
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>> > > > > > > >
>> > > > > > > _______________________________________________
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>> > > > > > >
>> > > > > >
>> > > > > >
>> > > > > > --
>> > > > > > *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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>> > > > >
>> > > >
>> > > >
>> > > > --
>> > > > *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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>> > --
>> > *PhD student*
>> > Institute of Biophysics of the CAS, v. v. i.
>> > Kralovopolska 135, 612 65 Brno
>> > _______________________________________________
>> > AMBER mailing list
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>> > 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
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Received on Mon Dec 16 2019 - 02:00:02 PST
