Hi Kanin,
I haven't tested ff19SB myself, so I am sure some other people might
comment on that with way more authority. As far as I am aware, the main
difference comes from CMAPs that should be loaded by leap. It could just be
that the FF is more sensitive to small distortions in your system? Until
someone with more experience with the ff answers, you could try using the
output structure from your ff14SB sims as input for leap, and reparametrize
it with ff19SB, and see if that works out?
Cheers,
El vie., 13 nov. 2020 a las 12:02, Kanin Wichapong (<
kanin.wichapong.gmail.com>) escribió:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
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Received on Sat Nov 14 2020 - 10:30:02 PST
