Re: [AMBER] AMBER20, ff19SB and OPC

From: Liao <liaojunzhuo.aliyun.com>
Date: Sat, 14 Nov 2020 13:07:40 -0600

Hi Kanin,
Last time I had the same problem of yours, I set vlimit=10 in the input file, and the problem goes away at 98% of the time.

Sent from my iPhone

> On Nov 14, 2020, at 12:21 PM, Stephan Schott <schottve.hhu.de> wrote:
>
> ´╗┐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>) escribi├│:
>>
>> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber


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Received on Sat Nov 14 2020 - 11:30:03 PST
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