Hi Carlos,
That’s the thing, the trajectory file (in ascii) contains only that frame. So if it was really the problem, Sander would go through also with imin = 5, but it is not the case.
I checked the energy of a different frame (the first one of my trajectory), with imin = 1 and imin = 5 and the energies don’t match at all after 50 stepsl. I am really clueless now… (Why are you setting up periodic condition when I tell you to not do it?!) So I guess I will have to go through each frame individually.
### Output 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
### Output imin = 5 ###
NSTEP ENERGY RMS GMAX NAME NUMBER
50 -5.6607E+03 5.5423E+00 7.8322E+01 O 3388
BOND = 541.7428 ANGLE = 769.3931 DIHED = 2506.6400
VDWAALS = 2494.5050 EEL = -22821.0985 HBOND = 0.0000
1-4 VDW = 825.6802 1-4 EEL = 9594.1609 RESTRAINT = 428.2861
EAMBER = -6088.9764
minimization completed, ENE= -.56606904E+04 RMS= 0.554225E+01
NetCDF error: NetCDF: Not a valid ID
at write time
NetCDF error: NetCDF: Not a valid ID
### 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-test.rst7 -y traj_split_10.nc
input: https://www.dropbox.com/s/anhry5lrc0mem8p/traj_min_10.inp
prmtop: https://www.dropbox.com/s/viduowi9uta424d/protein_system.prmtop
rst7: https://www.dropbox.com/s/j429pmsrppzeccb/protein_system.rst7
trajectory file: https://www.dropbox.com/s/94iltabu2lefwru/traj_split_10.nc
Thanks again for your help,
Jérôme
Le 16 déc. 2019 à 05:16, Carlos Simmerling <carlos.simmerling.gmail.com<mailto:carlos.simmerling.gmail.com>> a écrit :
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<mailto: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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Received on Mon Dec 16 2019 - 11:00:02 PST
