[AMBER] AMBER20, ff19SB and OPC

From: Kanin Wichapong <kanin.wichapong.gmail.com>
Date: Fri, 13 Nov 2020 11:57:49 +0100

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
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

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

equilibrate NPT 5ns
  cut=10.0, ntb=2, ntp=1, taup=2.0,
  ntpr=500, ntwx=500, ntwr = 500, ioutfm=1,
  ntt=3, gamma_ln=5.0,

I also tried the same input as in AMBER20 manual; but I still get same
error messages
>>> molecular dynamics run
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
AMBER mailing list
Received on Fri Nov 13 2020 - 03:00:02 PST
Custom Search