I'm not quite sure of the source of your problem. Could it be that the
input coordinates have very different box sizes? This is not normally the
case for input trajectories from MD, so it might be that sander sets things
up based on the first frame and then subsequent frames (since they are not
from MD) may be very different. If this is true then imin=5 may not work
and you'll need to use a script to calculate their energies separately.
Also make sure you are using the most recent version of the code, there may
have been changes to improve this behavior.
another possibility could be related to the restraints, maybe look at the
first step energies for this frame when you use imin=5 and when you isolate
the structure and use imin=1. do all of the energy terms match?
On Mon, Dec 16, 2019 at 12:24 AM Jerome Eberhardt <jerome.scripps.edu>
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/viduowi9uta424d/protein_system.prmtopprotein_system-min.rst7>:
> https://www.dropbox.com/s/ep62kx275iynbsx/protein_system-min.rst7
>
>
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>
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Received on Mon Dec 16 2019 - 05:30:02 PST
