Re: [AMBER] constant pH pmemd.cuda error

From: Cruzeiro,Vinicius Wilian D <vwcruzeiro.ufl.edu>
Date: Mon, 8 Oct 2018 21:20:08 +0000

Hello Andreas,


As you are doing the MD part in explicit solvent, the saltcon variable is only going to matter during the protonation state change attempts (which are made in implicit solvent). As the reference energies for the reference compounds were obtained with saltcon=0.1, you should keep this parameter unchanged in your simulation. Otherwise, in principle, you would need to recompute the reference energies for the new saltcon value you are using.


Talking about your problem: it seems that your simulation is crashing at around 3.3 ns. If you run the same simulation again, does it crash at the exact same spot? If so, did you try to set ntpr and ntwx close to 5 to see if you spot any misbehavior? A 500 interval might still be too large for this analysis.


Vinícius Wilian D Cruzeiro

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

Voice: +1(352)846-1633

________________________________
From: andreas.tosstorff.cup.uni-muenchen.de <andreas.tosstorff.cup.uni-muenchen.de>
Sent: Monday, October 8, 2018 5:03:26 PM
To: 'AMBER Mailing List'
Subject: Re: [AMBER] constant pH pmemd.cuda error

Thanks for your response! I am currently running with pmemd.MPI without any
error thus far.
Why do I have to keep saltcon=0.1? Isn't this dependent on the conditions I
want to simulate?

I should also mention that I am running Amber16 with the old cpin format.

Here's the last output from the pmemd.cuda:

NSTEP = 1667000 TIME(PS) = 4384.500 TEMP(K) = 297.13 PRESS =
0.0
 Etot = -65006.8876 EKtot = 16136.9229 EPtot =
-81143.8104
 BOND = 487.4047 ANGLE = 1514.2135 DIHED =
1876.0666
 1-4 NB = 622.2948 1-4 EEL = 6407.3247 VDWAALS =
9678.7089
 EELEC = -101729.8236 EHBOND = 0.0000 RESTRAINT =
0.0000

---------------------------------------------------------------------------- 
--
 NSTEP =  1667500   TIME(PS) =    4385.500  TEMP(K) =   301.90  PRESS =
0.0
 Etot   =    -64876.0673  EKtot   =     16395.9160  EPtot      =
-81271.9833
 BOND   =       516.0828  ANGLE   =      1455.9781  DIHED      =
1843.3318
 1-4 NB =       642.0154  1-4 EEL =      6337.0433  VDWAALS    =
9527.7712
 EELEC  =   -101594.2059  EHBOND  =         0.0000  RESTRAINT  =
0.0000
----------------------------------------------------------------------------
--
 NSTEP =  1668000   TIME(PS) =    4386.500  TEMP(K) =   301.08  PRESS =
0.0
 Etot   =    -64884.8785  EKtot   =     16351.5781  EPtot      =
-81236.4566
 BOND   =       552.6511  ANGLE   =      1449.2905  DIHED      =
1876.9476
 1-4 NB =       639.8351  1-4 EEL =      6468.3958  VDWAALS    =
9849.8281
 EELEC  =   -102073.4048  EHBOND  =         0.0000  RESTRAINT  =
0.0000
----------------------------------------------------------------------------
--
-----Original Message-----
From: Cruzeiro,Vinicius Wilian D <vwcruzeiro.ufl.edu>
Sent: Monday, October 8, 2018 10:34 PM
To: amber.ambermd.org
Subject: Re: [AMBER] constant pH pmemd.cuda error
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.
Best,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division University of Florida,
United States
Voice: +1(352)846-1633
________________________________
From: andreas.tosstorff.cup.uni-muenchen.de
<andreas.tosstorff.cup.uni-muenchen.de>
Sent: Monday, October 8, 2018 4:20:30 PM
To: amber.ambermd.org
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
kClearForces
cudaFree GpuBuffer::Deallocate failed an illegal memory access was
encountered”
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
&cntrl
  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,
  ntb=1,
  ntp=0
  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,
ntf=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
 <mailto:Andreas.Tosstorff.cup.uni-muenchen.de>
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Received on Mon Oct 08 2018 - 14:30:04 PDT
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