Re: [AMBER] NAN error

From: Bill Ross <ross.cgl.ucsf.edu>
Date: Mon, 21 Oct 2019 14:22:50 -0700

Hi Hira,

You could send the residue definition file and see if anyone spots a
problem, or build your molecule again and inspect the output closely for
warnings. Another experiment would be to place your residue by itself at
the edge of a small box of water, run until the image translates, and
see if the same problem occurs.

Except I think you said you are using continuum solvent which I haven't
used.. why would there even be a need for a box with a continuum solvent?

Bill


On 10/21/19 9:41 AM, Hira Jabeen wrote:
> Hi Bill,
> Yes there is a single non-standard molecule in my structure.
> Yes I am calculating energy (without water), in which I have ntb=0 and that is creating a separate problem.
> Here is the input and output file:
> Energy calculations on existing trajectory
> &cntrl
>  imin=5, maxcyc=1,
>  ntb=0,
>  ntpr=1, ntwr=10000000,
>  cut=999,
> &end
> Output:
>  Frac coord min, max:   -1.4568023624176908E-003  0.81675717401233827
>  The system has extended beyond
>      the extent of the virtual box.
>  Restarting sander will recalculate
>     a new virtual box with 30 Angstroms
>     extra on each side, if there is a
>     restart file for this configuration.
>  SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
>  Atom out of bounds. If a restart has been written,
>  restarting should resolve the error
>                                        Thanks,Hira
>
> On Monday, October 21, 2019, 04:02:16 PM GMT+1, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> 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 - 14:30:01 PDT
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