Hello everyone,
I am new to Amber simulations, but I want to figure out why I am getting
this error. :/
****************************************
Frac coord min, max: -3.0761577907135201E-006 0.96695690660196965
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
***************************************
I have attempted different step sizes and changing the size of the box, but
it still seems to error out. A lot of similar posts advise to watch the MD
simulation and figure out what is happening. Using my novice perception of
MD simulations, I think it is the waters that are leaving the box around
frame 9-10.
Here is my production input file:
****************************************
Implicit solvent molecular dynamics
&cntrl
imin=0, irest=1, ntx=5,
nstlim=7500000, dt = 0.002,
ntpr=1000, ntwx=1000, ntwr=1000,
cut=30.0, ntc=2, ntf=2,
ntb=0, ntp=0, taup=2.0,
ntt=3, temp0=300,
gamma_ln=2.0, ig=-1, ioutfm=1,
/
****************************************
Here is my md.out file:
***********************************************************************************************
NSTEP = 1000 TIME(PS) = 27.000 TEMP(K) = 301.73 PRESS =
0.0
Etot = -117222.2649 EKtot = 31078.4503 EPtot =
-148300.7153
BOND = 1139.0715 ANGLE = 3251.0412 DIHED =
4859.2594
1-4 NB = 1367.3768 1-4 EEL = 16749.3591 VDWAALS =
17507.0559
EELEC = -193173.8792 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 2000 TIME(PS) = 29.000 TEMP(K) = 301.98 PRESS =
0.0
Etot = -108428.1404 EKtot = 31104.9918 EPtot =
-139533.1322
BOND = 1199.9413 ANGLE = 3222.7152 DIHED =
4879.1025
1-4 NB = 1373.5198 1-4 EEL = 16804.6312 VDWAALS =
17399.0080
EELEC = -184412.0502 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 3000 TIME(PS) = 31.000 TEMP(K) = 299.56 PRESS =
0.0
Etot = -114024.6264 EKtot = 30855.7386 EPtot =
-144880.3651
BOND = 1245.8665 ANGLE = 3165.8670 DIHED =
4861.2191
1-4 NB = 1346.0351 1-4 EEL = 16766.7330 VDWAALS =
17521.9822
EELEC = -189788.0679 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 4000 TIME(PS) = 33.000 TEMP(K) = 299.81 PRESS =
0.0
Etot = -107519.4268 EKtot = 30880.6551 EPtot =
-138400.0819
BOND = 1138.7680 ANGLE = 3205.1196 DIHED =
4825.6560
1-4 NB = 1370.5540 1-4 EEL = 16841.8055 VDWAALS =
17260.7771
EELEC = -183042.7621 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 5000 TIME(PS) = 35.000 TEMP(K) = 300.90 PRESS =
0.0
Etot = -118357.7810 EKtot = 30993.2081 EPtot =
-149350.9891
BOND = 1195.8282 ANGLE = 3199.9498 DIHED =
4843.1400
1-4 NB = 1367.2846 1-4 EEL = 16811.4562 VDWAALS =
17541.2940
EELEC = -194309.9419 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 6000 TIME(PS) = 37.000 TEMP(K) = 300.20 PRESS =
0.0
Etot = -119199.0225 EKtot = 30921.6490 EPtot =
-150120.6715
BOND = 1140.8741 ANGLE = 3209.8834 DIHED =
4868.7171
1-4 NB = 1359.1385 1-4 EEL = 16796.7842 VDWAALS =
17306.8457
EELEC = -194802.9144 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 7000 TIME(PS) = 39.000 TEMP(K) = 299.72 PRESS =
0.0
Etot = -110588.1353 EKtot = 30871.3433 EPtot =
-141459.4786
BOND = 1154.2258 ANGLE = 3162.6286 DIHED =
4875.4965
1-4 NB = 1395.2825 1-4 EEL = 16899.3337 VDWAALS =
17104.6780
EELEC = -186051.1238 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 8000 TIME(PS) = 41.000 TEMP(K) = 298.15 PRESS =
0.0
Etot = -114274.1048 EKtot = 30709.9864 EPtot =
-144984.0912
BOND = 1211.6495 ANGLE = 3185.6529 DIHED =
4842.2165
1-4 NB = 1373.5635 1-4 EEL = 16854.0657 VDWAALS =
17533.6400
EELEC = -189984.8795 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 9000 TIME(PS) = 43.000 TEMP(K) = 302.71 PRESS =
0.0
Etot = -120148.4708 EKtot = 31179.9447 EPtot =
-151328.4155
BOND = 1175.4158 ANGLE = 3228.8444 DIHED =
4870.6552
1-4 NB = 1359.8866 1-4 EEL = 16748.4449 VDWAALS =
17806.4406
EELEC = -196518.1031 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
NSTEP = 10000 TIME(PS) = 45.000 TEMP(K) = 299.17 PRESS =
0.0
Etot = -113498.9083 EKtot = 30815.1102 EPtot =
-144314.0186
BOND = 1143.5996 ANGLE = 3166.6821 DIHED =
4904.0651
1-4 NB = 1384.2273 1-4 EEL = 16837.5777 VDWAALS =
17119.6262
EELEC = -188869.7966 EHBOND = 0.0000 RESTRAINT =
0.0000
------------------------------------------------------------------------------
Frac coord min, max: -3.0761577907135201E-006 0.96695690660196965
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
*************************************************************************************************
Please let me know what I should do. I have tried starting over, but it
usually crashes and I waste a couple days.
Thanks for everything.
--
Sincerely,
Miles Taylor
Graduate Student
Physical Chemistry
Department of Chemistry
Oregon State University
Corvallis, OR 97331
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Received on Mon Dec 19 2016 - 19:30:02 PST
