I am running a simulation of a protein with 576 residues, solvated
using TIP3P water model in a cubic box of 10 angstroms dimensions. The
whole system contains approximately 40000 atoms. I run the simulations
on NVIDIA GPU using PMEMD implementation of Amber 11.
In this simulation, I have to restrain almost the whole protein except
for some intermediate loop regions.. I performed the constant volume
and constant pressure equilibration steps separately and slowly
releasing the harmonic constraints on the loops while the rest of the
system is still constrained. As the last step of equilibration, I want
to run 500ps of unrestrained dynamics for the loops and the rest of
the protein should be restrained. I am pasting the input here.
# DYnamics with constant pressure with restraints at 300K for 500ps
&cntrl
imin=0,irest=1,ntx=5,
nstlim=250000,dt=0.002,
ntc=2,ntf=2,
cut=10, ntb=2, ntp=1, taup=1.0,
ntpr=500, ntwx=500,
ntt=3, gamma_ln=2.0,
temp0=300.0,
ntr=1,
/
Restraints
2.0
RES 1 45
END
rest
2.0
RES 59 134
END
rest
2.0
RES 153 270
END
rest
2.0
RES 289 333
END
rest
3.0
RES 347 422
END
restr
2.0
RES 441 558
END
END
When the whole protein is restrained the simulations were running
properly and when a part of the system is constrained I get the
following error in the terminal whereas no errors are printed in the
mdout file.
cudaMalloc GpuBuffer::Allocate failed out of memory
At line 111 of file inpcrd_dat.f90
Fortran runtime error: End of file
or
cudaMemcpyToSymbol: SetSim copy to cSim failed all CUDA-capable devices are busy
or unavailable
At line 111 of file inpcrd_dat.f90
Fortran runtime error: End of file
I did some trials by removing and adding the restraints one at a time...
with the first three restraint groups, the process runs whereas when
the last three groups are used individually or in combination with the
first three, the process fails with the errors...
When i checked the pdb file extracted from the restart file of
previous run, i do not see any strange behaviour of protein or waters.
The rms difference is less than 0.9 from the initial structure.
It would be grateful if anyone can tell me where I am going wrong and
help me solve this problem...
--
Sangeetha
Pondicherry University
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Received on Mon Aug 08 2011 - 23:30:04 PDT
