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
