You could always switch to ntpr=1, ntwx=1 and view the trajectory for
possibly interpretable drama.
There may be a clue in the change from your previous input file.
Bill
On 8/23/18 1:18 AM, Helena Damtoft Tjørnelund 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 Thu Aug 23 2018 - 01:30:03 PDT
