Re: [AMBER] NAN error

From: Hira Jabeen <hira_bioinfo.yahoo.com>
Date: Mon, 21 Oct 2019 14:14:14 +0000 (UTC)

 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 - 07:30:02 PDT
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