Re: [AMBER] constant pH pmemd.cuda error

From: Cruzeiro,Vinicius Wilian D <>
Date: Mon, 8 Oct 2018 20:34:09 +0000

Hello Andreas,

This is a CUDA error. Did you try setting icnstph=0 to see if the problem persists? Do you have any errors if you run the same calculation with pmemd.MPI?

Could you copy here the bottom of your mdout file, before the calculation fails?

Side note: you should be running your simulation with saltcon=0.1, but this shouldn't be the source of your error.


Vinícius Wilian D Cruzeiro

PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States

Voice: +1(352)846-1633

From: <>
Sent: Monday, October 8, 2018 4:20:30 PM
Subject: [AMBER] constant pH pmemd.cuda error

Hi all,

I am trying to run an explicit solvent constant pH simulation with
pmemd.cuda which constantly fails after a few ns giving the following error:

“Error: an illegal memory access was encountered launching kernel

cudaFree GpuBuffer::Deallocate failed an illegal memory access was

I already tried reducing ntpr and ntwx to look for anything pointing to the
problem, but couldn’t find anything. The system is a protein and approx.
26000 atoms.

I already started a run using pmemd.MPI to get a more verbose error message.

I am titrating all HIP, AS4, GL4 residues, giving a total of 24.

I’d really appreciate any advice to identify the problem.

My input file:

production phase, NVT, 250 ns


  imin = 0,

  ntx = 5,

  irest = 1,

  ntpr = 500,

  ntwr = 625000,

  ntwe = 2500,

  ntwx = 500,

  ntwprt = 2786,

  ioutfm = 1,

  iwrap = 1,

  cut = 9.0,

  ntt = 3,



  temp0 = 300,

  gamma_ln = 1.0,

  ig = -1,

  nstlim = 125000000,

  dt = 0.002,

  icnstph=2, ntcnstph=100, ntrelax=200, solvph=5.0, saltcon=0.001, ntc=2,


Andreas Tosstorff, M.Sc. Chemistry, PhD Student

Ludwig-Maximilians-University Munich

Department of Pharmacy

Pharmaceutical Technology & Biopharmaceutics

Butenandtstr. 5
D-81377 München

Tel: +49 89 2180 77059

Fax: +49 89 2180 77020


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Received on Mon Oct 08 2018 - 14:00:03 PDT
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