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 - 10:00:01 PDT
