Hi
Do you want to use implicit or explicit water?
If explicit water, you need to update ntb value.
If implicit water, you need to specify igb value.
How did you build your structure?
If you are new to simulation, did you try to reproduce amber tutorial yet?
Hai Nguyen
> On Dec 19, 2016, at 10:11 PM, Taylor, Miles <taylormi.oregonstate.edu> wrote:
>
> 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 - 22:30:02 PST
