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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 03 2012 - 00:00:03 PDT
