Could you please show us your CPIN file?
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633<tel:+1(352)846-1633>
On Aug 24, 2018, at 5:47 AM, Helena Damtoft Tjørnelund <s153842.student.dtu.dk<mailto:s153842.student.dtu.dk>> wrote:
Hello Vinicius, Jason, Bill,
Thank you for your comments.
I did try all you of your suggestions.
I tried running a few steps of production run using pmemd.mpi (around 2000 frames)and then switching to pmemd.cuda. It still crashes at exactly 500th step.
Just running my system using pmemd.MPI takes about 3000hours for 100ns.
Best regards
Helena
________________________________
Fra: Cruzeiro,Vinicius Wilian D <vwcruzeiro.ufl.edu<mailto:vwcruzeiro.ufl.edu>>
Sendt: 24. august 2018 10:52:42
Til: AMBER Mailing List
Emne: Re: [AMBER] Problems with constant pH production step
Hello Helena,
I see you are setting saltcon=0.0. Try setting saltcon=0.1.
Best,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633<tel:+1(352)846-1633>
On Aug 24, 2018, at 2:42 AM, Helena Damtoft Tjørnelund <s153842.student.dtu.dk<mailto:s153842.student.dtu.dk><mailto:s153842.student.dtu.dk>> wrote:
I'm using pmemd.cuda in AMBER 16, but I have also tried with AMBER 18.
Furthermore, if I use the restart files from the last step where the protein is present (frame 498) and restart the simulation, I can get it to run for another 500 steps before the protein disappears again.
BR,
Helena
________________________________
Fra: Jason Swails <jason.swails.gmail.com<mailto:jason.swails.gmail.com><mailto:jason.swails.gmail.com>>
Sendt: 23. august 2018 16:48:45
Til: AMBER Mailing List
Emne: Re: [AMBER] Problems with constant pH production step
What program are you using?
--
Jason M. Swails
On Aug 23, 2018, at 4:18 AM, Helena Damtoft Tjørnelund <s153842.student.dtu.dk<mailto:s153842.student.dtu.dk><mailto:s153842.student.dtu.dk>> wrote:
Hello AMBER community,
I am trying to do a constant pH simulation on a protein, but during the production step an error occurs. After 500 steps something goes wrong, as seen below:
wrapping first mol.: 57.92036 81.91175 141.87531
wrapping first mol.: 57.92036 81.91175 141.87531
NSTEP = 400 TIME(PS) = 5001.796 TEMP(K) = 299.67 PRESS = 0.0
Etot = -971786.4313 EKtot = 237328.6719 EPtot = -1209115.1032
BOND = 3999.2974 ANGLE = 10605.4152 DIHED = 14122.9759
1-4 NB = 4762.1390 1-4 EEL = 58004.2211 VDWAALS = 172178.1361
EELEC = -1472787.2880 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
wrapping first mol.: NaN NaN NaN
wrapping first mol.: NaN NaN NaN
NSTEP = 500 TIME(PS) = 5001.996 TEMP(K) = 786.75 PRESS = 0.0
Etot = ************** EKtot = 623078.6875 EPtot = **************
BOND = 26775.7612 ANGLE = 27621.9031 DIHED = 13707.5247
1-4 NB = ************** 1-4 EEL = 57695.9679 VDWAALS = 3252.9726
EELEC = -8428935.9376 EHBOND = 0.0000 RESTRAINT = 0.0000
------------------------------------------------------------------------------
My input file for the production step is shown below. I have tried different combinations of ntwr, ntpr, and ntwx, but this does not fix the problem - no matter what the error occurs around 500 steps.
Explicit solvent constant pH MD
&cntrl
imin=0, irest=1, ntx=5, ntxo=2,
ntwr=100 ,ntpr=100, ntwx=100, nstlim=1000,
dt=0.002, ntt=3, tempi=300,
temp0=300, gamma_ln=5.0, ig=-1,
ntc=2, ntf=2, cut=8, iwrap=1,
ioutfm=1, icnstph=2, ntcnstph=500,
solvph=7.5, ntrelax=100, saltcon=0.0,
/
Thank you - Best Regards
Helena Damtoft T.
Technical University of Denmark
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Received on Fri Aug 24 2018 - 03:30:02 PDT
