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 - 21:30:02 PST
