Re: [AMBER] NAN error

From: Bill Ross <ross.cgl.ucsf.edu>
Date: Mon, 21 Oct 2019 08:01:50 -0700

Do you have a nonstandard residue in 1st molecule? If so, I'd check it
carefully.

The mdin looks ok, but w/out solvent model experience or running
anything recently.

Bill

On 10/21/19 7:14 AM, Hira Jabeen wrote:
> Hi Bill,
> Above were two different output files (different chunks of 10ns) means:Note the temp goes from ok to NaN between step 1500 and
> step 500,this isn't the case, I guess it goes wrong from entire 10ns.
> I will try to run a short simulation from last restart file with saving each step.
> So there is nothing wrong in the mdin file, topology file has something wrong???
> Thanks,Hira
> On Monday, October 21, 2019, 02:46:13 PM GMT+1, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> I've never used the solvent model, so will do my favorite thing, guess
> in the dark. Note the temp goes from ok to NaN between step 1500 and
> step 500, implying restarting a run occurred, a possible clue, but first
> I'd consider "wrapping first mol.: NaN            NaN" - evidently a
> molecule was translated at a box boundary, which might indicate
> something unusual about the topology of your first molecule, e.g.
> never-before-encountered-by-code or, more typically, naive user error in
> a self-defined residue.
>
> One obvious thing to try when stumped is rerun from last saved restrt,
> and save each step mdcrd/mdout for detailed analysis. Some may even find
> the frames leading up to NaN moving in unforeseeable, life-changing
> ways. :-)
>
> Bill
>
>
> On 10/21/19 6:33 AM, Hira Jabeen wrote:
>> =============================================================================== NSTEP =     1500   TIME(PS) =   11463.000  TEMP(K) =   299.84  PRESS =     0.0
>>    Etot   =   -119172.6971  EKtot   =     27004.0586  EPtot      =   -146176.7557
>>    BOND   =       827.6985  ANGLE   =      2136.0365  DIHED      =      2534.8472
>>    UB     =       244.8267  IMP     =       137.2601  CMAP       =      -112.0989
>>    1-4 NB =       626.2361  1-4 EEL =      8757.7227  VDWAALS    =     11736.4103
>>    EELEC  =   -173065.6950  EHBOND  =         0.0000  RESTRAINT  =         0.0000
>> But in further simulations, it gives NaN and then stops...
>>
>> ------------------------------------------------------------------------------
>>      4.  RESULTS
>> -------------------------------------------------------------------------------- ---------------------------------------------------
>>    APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
>>    using   5000.0 points per unit in tabled values
>>    TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
>> | CHECK switch(x): max rel err =   0.2738E-14   at   2.422500
>> | CHECK d/dx switch(x): max rel err =   0.8332E-11   at   2.782960
>>    ---------------------------------------------------
>> |---------------------------------------------------
>> | APPROXIMATING direct energy using CUBIC SPLINE INTERPOLATION
>> |  with   50.0 points per unit in tabled values
>> | Relative Error Limit not exceeded for r .gt.   2.47
>> | APPROXIMATING direct force using CUBIC SPLINE INTERPOLATION
>> |  with   50.0 points per unit in tabled values
>> | Relative Error Limit not exceeded for r .gt.   2.89
>> |---------------------------------------------------
>> wrapping first mol.:            NaN            NaN            NaN NSTEP =      500   TIME(PS) =   54961.000  TEMP(K) =      NaN
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Received on Mon Oct 21 2019 - 08:30:03 PDT
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