It seems it's trying to use ewald when imin=5, in case it helps debug /
work around - is there another flag that also turns off ewald?
Not a real Molecular Dietician, I just play one on the net.
Bill
On 12/15/19 9:24 PM, Jerome Eberhardt wrote:
> Hi Amber users,
>
> I know that the virtual box is a recurrent question on the forum, but I cannot wrap my head around this specific problem.
>
> I am currently trying to minimize a whole trajectory (imin = 5) produced by a completely different process (not MD). And sometime, it does not work because during the minimization process it seems that one of the atoms is going beyond the virtual box. But if I isolate this particular frame and run again the minimization with imin = 1, it goes through without any problem. Why?
>
> I tried to use igb = 6 with imin = 5, it does not work neither and if I do the minimization with imin = 1 and igb = 6, it gives me a completely different result at the end, with a positive final energy.
>
> Thanks for your help,
>
> Jérôme.
>
>
>
> ## COMMAND LINE ##
> sander -O -i min.inp -o min.out -p protein_system.prmtop -c protein_system.rst7 -ref protein_system.rst7 -x protein_system-min.rst7 -y protein_system.rst7
>
> ## INPUT IMIN = 1 ##
> Minimization of solvent orientation
> &cntrl
> imin = 1, ! imin
> maxcyc = 50, ! (maxcyc - ncyc) steps of CONJ
> ntmin = 0, ! CONJ
> ntb = 0, ! No periodic box, PME is off
> igb = 0, ! In vacuum electrostatics
> cut = 9, ! Non-bonded cutoff
> nsnb = 50, ! Non-bonded list update every 100 steps
> ntc = 1, ! No SHAKE
> ntf = 1, ! Force evaluation, complete interaction is calculated
> ntr = 1, ! Use harmonic constraints
> restraint_wt = 2.5, ! Constraints of 2.5 kcal/mol
> restraintmask = '!.H= & !:WAT', ! Constraints of heavy atoms except WAT
> ntx = 1, ! No velocities in the inpcrd file
> ntwx = 50, ! Every ntwx steps, the coordinates will be written to the mdcrd file
> ioutfm = 0 ! Binary NetCDF trajectory
> /
>
> ## OUTPUT FINAL ENERGY IMIN = 1 ##
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 50 -3.9771E+03 5.8922E+00 1.0709E+02 H1 4340
>
> BOND = 546.2850 ANGLE = 923.4480 DIHED = 2521.1605
> VDWAALS = 2749.6095 EEL = -21571.2602 HBOND = 0.0000
> 1-4 VDW = 872.4954 1-4 EEL = 9640.5688 RESTRAINT = 340.6237
> EAMBER = -4317.6932
>
> ## INPUT IMIN = 5 ##
> Minimization of solvent orientation
> &cntrl
> imin = 5, ! Apply to every frame in the input traj
> maxcyc = 50, ! (maxcyc - ncyc) steps of CONJ
> ntmin = 0, ! SD + CONJ
> ntb = 0, ! No periodic box, PME is off
> igb = 0, ! In vacuum electrostatics
> cut = 9, ! Non-bonded cutoff
> nsnb = 50, ! Non-bonded list update every 100 steps
> ntc = 1, ! No SHAKE
> ntf = 1, ! Force evaluation, complete interaction is calculated
> ntr = 1, ! Use harmonic constraints
> restraint_wt = 2.5, ! Constraints of 2.5 kcal/mol
> restraintmask = '!.H= & !:WAT', ! Constraints of heavy atoms except WAT
> ntx = 1, ! No velocities in the inpcrd file
> ntwx = 50, ! Every ntwx steps, the coordinates will be written to the mdcrd file
> ioutfm = 0 ! Binary NetCDF trajectory
> /
>
> ## OUTPUT FINAL ENERGY IMIN = 5 ##
> Frac coord min, max: 0.24816694982858301 7.9791926973270986
> 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
>
> protein_system.rst7: https://www.dropbox.com/s/j429pmsrppzeccb/protein_system.rst7<https://pastebin.com/XQhy36RM>
> protein_system.prmtop: https://www.dropbox.com/s/viduowi9uta424d/protein_system.prmtop
> protein_system-min.rst7: https://www.dropbox.com/s/ep62kx275iynbsx/protein_system-min.rst7
>
>
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Received on Sun Dec 15 2019 - 22:30:02 PST
