Re: [AMBER] Problems with constant pH production step

From: Helena Damtoft Tjørnelund <s153842.student.dtu.dk>
Date: Fri, 24 Aug 2018 09:47:18 +0000

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>
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>> 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>>
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>> 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 - 03:00:02 PDT
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