Hi Raquel,
I suspect you have some kind of atom clashes in your system and this is causing the GPU code to crash. You could try running this with the CPU version and see what happens - you could also try setting ntpr=1 and ntwx=1 (and maybe reduce nstlim to 500 or so) and then look closely at the output / visualize things and see if anything looks wrong. A typical example where this happens is when you get a lipid tail that is effectively threaded through a phenyl ring of the protein. Look for things like this since minimization will not fix this problem.
All the best
Ross
> On Feb 26, 2015, at 6:02 PM, Romero, Raquel <raquel.romero.12.ucl.ac.uk> wrote:
>
> Dear all,
>
>
> I have gone through all the mailing list and I havenīt been able to find the answer for my problem.
>
>
> I want to run a MD over a system composed by a lipid membrane, two proteins, and the ligand of one of them, I have set up my system using antechamber and Lipid 14. Everything looks alright. After two EM (one for minimization for water and ions) and the other for the whole system (50000 cycles of minimization), I tried to heat up the system using the following input file:
>
>
> (I have done the same process before with one protein plus membrane and everything went well including the 250 ns production).
>
>
> Heating 100K
> &cntrl
> imin=0,
>
> ntx=1,
> irest=0,
> ntc=2,
> ntf=2,
> tol=0.0000001,
> nstlim=5000,
> ntt=3,
> gamma_ln=1.0,
> ntr=1,
> ig=-1,
> ntpr=100,
> ntwr=10000,
> ntwx=250,
> dt=0.002,
> nmropt=1,
> ntb=1,
> ntp=0,
> cut=12.0,
> ioutfm=1,
> ntxo=2,
> /
> &wt
> type='TEMP0',
> istep1=0,
> istep2=5000,
> value1=0.0,
> value2=100.0 /
> &wt type='END' /
> Hold lipid and prot fixed
> 10.0
> RES 1 1781
> END
> END
>
>
> I am getting the following error: Error: an illegal memory access was encountered launching kernel kClearForces. cudaFree GpuBuffer::Deallocate failed an illegal memory access was encountered.
>
> 1. I tried it without restraints which was also suggested somewhere else.
>
> 2. I donīt think it is nothing to be with the GPU suitability as is suggested in other emails.
>
> 3. Looking at the outputs of the EM everything seems pretty normal including the graphical output.
>
>
> Any suggestions may help.
>
> Thanks a lot for your time and help
>
> Raquel
>
>
>
>
> Raquel Romero
> Department of Pharmaceutical and Biological Chemistry
> UCL School of Pharmacy, University College London
> 29/39 Brunswick Square
> London
> WC1N 1AX
>
> T: 0207 753 5972
> E: raquel.romero.12.ucl.ac.uk
>
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Received on Thu Feb 26 2015 - 20:00:03 PST
