how big is your periodic box?
I've no definite answer, but it sounds like because of the constant
pressure, at some point your periodic box shrinks to the point that an 8
angstrom cutoff now spans across a periodic cell. So, as 8 angstroms is
already kind of a bare minimum for cutoff I would say, you should solvate
your system with more water and therefore a larger periodic cell.
maybe that's not the issue though.
~Aron
On Thu, May 3, 2012 at 2:50 AM, Agostino Bruno <agostino.bruno.nemo.unipr.it
> wrote:
> Dear all,
>
> I am running a simulation of a small globular protein in an explicit water
> box, using the CUDA version
> of pmemd.
>
> |--------------------- INFORMATION ----------------------
> | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> | Version 2.2
>
>
> Below the input script:
>
> MD with cartesian restraints (NPT ensemble) LD
> &cntrl
> imin=0, irest=1, ntx=5,
> iwrap=1,
> ntb=2,
> ntp=1, pres0=1.0, taup=1.0,
> ntt=3, temp0=310.0, gamma_ln=5.0,
> ntc=2, ntf=2, dt=0.002,
> cut=8.0,
> nstlim=5000000,
> ntwe=10000, ntwx=10000, ntpr=10000,
> /
>
> The simulation run without any problem until 1360000 step (about 2.6 ns),
> at this point amber stop
> to work, and in the output files this error appears:
>
>
> | ERROR: max pairlist cutoff must be less than unit cell max sphere
> radius!
>
>
> Checking the energy of the system every things seem ok:
>
> NSTEP = 1360000 TIME(PS) = 2970.000 TEMP(K) = 309.21 PRESS =
> 26.8
> Etot = -118659.5868 EKtot = 29291.0117 EPtot =
> -147950.5986
> BOND = 899.9715 ANGLE = 2411.0275 DIHED =
> 3117.2117
> 1-4 NB = 1088.2575 1-4 EEL = 11955.7535 VDWAALS =
> 17116.3750
> EELEC = -184539.1953 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 13001.3279 VIRIAL = 12730.3217 VOLUME =
> 468077.8731
> Density =
> 1.0158
>
> If I used the last restart file (when the simulation is stopped) with ntpr
> = 1 the system run again,
> withouth any problems (i tried for 20000 steps about 40ps), if I use ntpr
> = 10000 the simulation
> never start again. Here the energy of the last 20000 steps:
>
>
> A V E R A G E S O V E R 20000 S T E P S
>
>
> NSTEP = 20000 TIME(PS) = 3014.000 TEMP(K) = 310.00 PRESS =
> 3.4
> Etot = -118563.8401 EKtot = 29366.3314 EPtot =
> -147930.1715
> BOND = 897.1811 ANGLE = 2398.1512 DIHED =
> 3104.8438
> 1-4 NB = 1085.6684 1-4 EEL = 11960.3477 VDWAALS =
> 17149.1103
> EELEC = -184525.4740 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 12993.6321 VIRIAL = 12959.1132 VOLUME =
> 469025.7679
> Density =
> 1.0138
>
> ------------------------------------------------------------------------------
>
>
> R M S F L U C T U A T I O N S
>
>
> NSTEP = 20000 TIME(PS) = 3014.000 TEMP(K) = 1.37 PRESS =
> 107.4
> Etot = 213.2870 EKtot = 129.7872 EPtot =
> 173.3394
> BOND = 25.3939 ANGLE = 38.3328 DIHED =
> 21.7654
> 1-4 NB = 13.9034 1-4 EEL = 33.9329 VDWAALS =
> 157.6135
> EELEC = 245.4382 EHBOND = 0.0000 RESTRAINT =
> 0.0000
> EKCMT = 86.0799 VIRIAL = 1090.4665 VOLUME =
> 534.4090
> Density =
> 0.0012
>
> ------------------------------------------------------------------------------
>
>
>
>
> I also visually checked the system, which not blows up neither at 1360000,
> or in the subsequent
> 20000 steps.
>
> Which could be my problem?
>
> Thank you very much for your attention and collaboration,
>
>
> Agositno
>
>
> --
> Agostino Bruno, PhD
> Dipartimento Farmceutico
> Universita' degli Studi di Parma
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Thu May 03 2012 - 09:30:04 PDT
