Yeap... This is the NTB=2, ntr=1 bug. The fix really is coming soon.
As I say for now either do not use restraints (why do you want restraints
after the equilibration anyway?) or set ntb=1 and run with NVT.
All the best
Ross
> -----Original Message-----
> From: arikcohen [mailto:arikcohen.ucla.edu]
> Sent: Thursday, August 11, 2011 3:54 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] unspecified launch failure launching kernel
> kCalculateMolecularVirial
>
> Sorry, here is the eq.in
>
> equilibration run (0 - 2 ns)
> &cntrl
> imin=0, ! No minimization, plain MD(default)
> irest=1, ! restart calculation
> ntx=5, ! Read X and V formatted, if ntb > 0 read
> box,
> use V if irest = 1
> ntb=2, ! Use pbc Pressure = const
> pres0=1.0, ! Reference pressure
> ntp=1, ! constant pressure dynamics
> taup=2.0, ! Pressure relaxation time
> cut=10, ! Non-bonded interaction cutoff
> ntc=2, ! SHAKE: Constrain bonds involving H atoms
> ntf=2, ! Typically ntf=ntc enable TIP3P constrain
> tempi=300.0, temp0=300.0, ! Initial and final(reference) temperature if
> ntt>0
> ntt=3, ! Switch temperature scaling (3 Use Langevin
> dynamics)
> gamma_ln=1.0, ! Collision frequency for Langevin dynamics
> nstlim=1000000, dt=.002, ! Number of MD steps and step size(in ps)
> ntpr=100, ! Print energy every
> ntwx=100, ! Print coor every
> ntwr=500, ! Print for restart option every
> ntr=1, ! Restrain atoms(cartesian space) using
> harmonic potentail
> &end
> Group input for restrained atoms
> 30
> RES 1 8
> RES 10
> RES 12 47
> RES 49
> RES 51 99
> RES 101 126
> RES 128 199
> RES 201 220
> RES 222 248
> END
> END
>
> Thanks a lot again,
>
> Arik
>
> On 8/11/2011 3:12 PM, Ross Walker wrote:
> > Hi Arik,
> >
> > Please send you input files. I suspect the bug is NPT + restraints
> which is
> > fixed in our development tree. Just waiting some final testing before
> > release.
> >
> > For now you can run NVT and you should be fine.
> >
> > All the best
> > Ross
> >
> >> -----Original Message-----
> >> From: arikcohen [mailto:arikcohen.ucla.edu]
> >> Sent: Thursday, August 11, 2011 3:05 PM
> >> To: AMBER Mailing List
> >> Subject: Re: [AMBER] unspecified launch failure launching kernel
> >> kCalculateMolecularVirial
> >>
> >> No. just a regular enzyme-substrate calculation.
> >>
> >> Arik
> >>
> >> On 8/11/2011 3:03 PM, Scott Le Grand wrote:
> >>> Organic solvent or lipid bilayer simulation by any chance?
> >>> On Aug 11, 2011 2:59 PM, "arikcohen"<arikcohen.ucla.edu> wrote:
> >>>> Dear Users,
> >>>>
> >>>> While running on a GPU cluster I encountering from time time the
> >>>> following persistent error:
> >>>>
> >>>> *unspecified launch failure launching kernel
> >> kCalculateMolecularVirial*
> >>>> I would be most thankful for any help/suggestion you might have.
> >>>>
> >>>> Thanks,
> >>>>
> >>>> Arik
> >>>>
> >>>>
> >>>>
> >>>> _______________________________________________
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> >>
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Received on Thu Aug 11 2011 - 16:30:03 PDT
