Dear AMBER users and developers,
I recently installed AMBER20 on my computer (ubuntu20, GeForce GTX 1080,
Nvidia Driver Version: 455.38 and CUDA Version: 10) and it went well, all
tests during installation didn't show any errors. However, I have problems
to run simulations using the new ff (ff19SB) and water model (OPC).
By using ff19SB with OPC, at some points during simulations I always get
error messages;
cudaMemcpy GpuBuffer::Download failed an illegal memory access was
encountered
or
ERROR: Calculation halted.
I already searched for the solutions and tried different settings, slowly
heating and equlibrating the systems and during these phases, it went well.
But then I always got error messages during the production run.
However, if I use ff14SB with OPC for the same system with the same
settings, simulations went fine (no problems, no error messages).
Do I have to set some special parameters for ff19SB & OPC during tleap or
simulations?
here are my tleap and input fo production run;
>> tleap
source leaprc.protein.ff19SB
source leaprc.water.opc
com = loadpdb cplx-input.pdb
solvateBox com OPCBOX 10.0
check com
addions com Na+ 0
check com
saveamberparm com cplx-sol.prmtop cplx-sol.mdcrd
savepdb com cplx-sol.pdb
quit
>>>production-run.in
equilibrate NPT 5ns
&cntrl
imin=0,irest=1,ntx=5,
nstlim=2500000,dt=0.002,
ntc=2,ntf=2,ig=-1,
cut=10.0, ntb=2, ntp=1, taup=2.0,
ntpr=500, ntwx=500, ntwr = 500, ioutfm=1,
ntt=3, gamma_ln=5.0,
temp0=300.0,
/
I also tried the same input as in AMBER20 manual; but I still get same
error messages
>>> molecular dynamics run
&cntrl
imin=0, irest=1, ntx=5, (restart MD)
ntt=3, temp0=300.0, gamma_ln=5.0, (temperature control)
ntp=1, taup=2.0, (pressure control)
ntb=2, ntc=2, ntf=2, (SHAKE, periodic bc.)
nstlim=500000, (run for 0.5 nsec)
ntwx=1000, ntpr=200, (output frequency)
/
Best regards,
Kanin Wichapong
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Received on Fri Nov 13 2020 - 03:00:02 PST
