Hi Raquel,
Throughout my journeys with membrane protein simulation I've encountered this error many times.
Look at your energy minimization outputs, for vdwaals, or any other parameters for that matter, show xxxxxxx? Even if your system is showing energy minimization as expected, there are some atom clashes which cannot be resolved using amber EM. Although, I once had luck performing implicit solvent EM and then using that system to build following the current tutorial.
I'm currently writing a newer, easier and more robust protocol to build and run membrane protein systems which should be available in the next week or so. I'll be posting this to the AMBER mailing list.
Best,
Parker
________________________________________
From: Romero, Raquel [raquel.romero.12.ucl.ac.uk]
Sent: Thursday, February 26, 2015 9:02 PM
To: amber.ambermd.org
Subject: [AMBER] CUDA- Error pmemd Lipid Membrane
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 - 19:30:02 PST
