Hi Wen,
This error likely means something is wrong with your simulation and it is blowing up. Firstly did you run the minimization on the GPU or the CPU? If GPU then I recommend going back and running the minimization on the CPU and see if that fixes things. The fixed precision used in the GPU code means that minimization fails (silently) for highly strained systems so it is recommended that this be run on the CPU. That may be your problem and a CPU minimization may clean things up such that the heating then works. If it doesn't then I recommend running the heating on the CPU but set ntpr=1,ntwx=1 and nstlim=100. You can then visualize this 100 step trajectory and see if there are any obvious problems.
One other note is a restraint (note restraint not constraint as you have it labelled) of 200.0 kcal/mol/A is probably way too high. Something on the order of 10.0 should be plenty.
All the best
Ross
> On Apr 18, 2017, at 12:02 PM, Li, Wen <wl2290.cumc.columbia.edu> wrote:
>
> Hi Everyone,
>
> I am running pmemd.cuda on an Amber Certified High-End workstation with a 24GB P6000 Quadro card. The solvated system includes about 800,000 atoms. Running minimization worked, but running heating got the error message as the following. I am wondering if the molecular system is too large to use this workstation.
>
> Error: an illegal memory access was encountered launching kernel kC learForces
> cudaFree GpuBuffer::Deallocate failed an illegal memory access was encountered
>
> Here is my input file:
>
> heat NVT 50ps
> &cntrl
> imin=0, irest=0, ntx=1,
> nstlim=25000, dt=0.002,
> ntc=2, ntf=2, cut=8.0,
> ntt=3, gamma_ln=1.0,
> ntb=1, ntp=0,ig = -1,
> tempi=0.0, temp0=300.0,
> ntpr=1000, ntwx=1000, ntwr=1000, ntwprt=83374,
> ioutfm=1,
> /
> Constraints
> 200.0
> RES 1 5149
> END
> END
>
> Thank you!
> Wen
>
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Received on Tue Apr 18 2017 - 10:30:02 PDT
