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Author: Admin | 2025-04-28
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 usedMinimize 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,_______________________________________________AMBER mailing listAMBER.ambermd.orghttp://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Mar 23 2022 - 22:30:02 PDT
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