Re: [AMBER] Problems with constant pH production step

From: Helena Damtoft Tjørnelund <s153842.student.dtu.dk>
Date: Fri, 24 Aug 2018 06:41:15 +0000

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>
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> 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 - 00:00:01 PDT