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
