Dear Amber users,
During my MD run I got such as error about shake, please see below
---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using 5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
---------------------------------------------------
| Local SIZE OF NONBOND LIST = 1468479
| TOTAL SIZE OF NONBOND LIST = 21413472
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -351381.5964 EKtot = 0.0000 EPtot = -351381.5964
BOND = 251.5921 ANGLE = 1235.1768 DIHED = 1604.5703
1-4 NB = 1314.9823 1-4 EEL = 13887.0078 VDWAALS = 56065.2558
EELEC = -425740.1815 EHBOND = 0.0000 RESTRAINT = 0.0000
Ewald error estimate: 0.6214E-04
------------------------------------------------------------------------------
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 8 14 192 190
my input file was:
equilibration
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 9,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0.0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 10.0, vlimit=5,
nstlim = 10000, dt = 0.002,
ntpr = 50, ntwx = 50, ntwr = 50
/
Keep protein with the weak restraints
10.0
RES 1-380
END
END
minimization steps worked without any problems, should I change something in this input file?
/Urszula
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Received on Wed May 16 2012 - 04:00:03 PDT
