Dear Amber users,
I am trying to simulate a protein in water. I have successfully
generated the topology (.top) and coordinate (.rst) files using tleap.
I am getting the following error while minimization, particularly in the
minimization of water.
cudaMemcpy GpuBuffer::Download failed an illegal memory access was
encountered.
And this didn't give results in the output file (min_wat.out) and didn't
generate the coordinate file.
I used the following command for minimization:
pmemd.cuda -O -i min_wat.in -o min_wat.out -p job_solv.top -c
job_solv.rst -r min_wat.rst -ref job_solv.rst.
----------------------------------------------------------------------------------------------------
Here is the min_wat.in, I used
Minimize water
System minimization:
&cntrl
imin=1, ntmin=1, nmropt=0, drms=0.1,
maxcyc=10000, ncyc=7000,
ntx=1, irest=0,
ntpr=500, ntwr=500, iwrap=0,
ntf=1, ntb=1, cut=5.0, nsnb=5,
igb=0,
ibelly=0, ntr=1,
restraintmask="!:WAT", restraint_wt=10.0,
&end
/
----------------------------------------------------------------------------------------------------
I also tried the same for 3 steps using pmemd.cuda (setting ntpr=ntwr=1)
but the same problem popped up.
When I did it using the sander.MPI and it worked.
Can someone explain, why it's showing problems with pmemd.cuda.
Thanks and regards,
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Received on Wed Mar 23 2022 - 22:30:02 PDT
