Dear Sir,
I have problem about ewald error estimate during equilibration run. So
please tell me whether i am wrong in setting parameter for equilibration or
have any problem in input file. I have created .prepin and frcmod file for
modified nucleosides by using .gaff force field in antechamber. so it is
write for performing equlibration md and production md.
my input file for equlibration is here:
imin=0, irest=0, ntx=1,
ntb=1, cut=9.0, ntr=1,
ntc=2, ntf=2, tempi=0.0, temp0=300.0,
ntt=3, gamma_ln=1.0,
nstlim=10000, dt=0.002,
ntpr=250, ntwx=250,ntwr=10000
/
Keep DNA fixed with weak restraint
10.0
RES 1 20
END
END
error is as follows:
Local SIZE OF NONBOND LIST = 3118967
| TOTAL SIZE OF NONBOND LIST = 3118967
NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0
Etot = -62975.0295 EKtot = 0.0000 EPtot = -62975.0295
BOND = 21.0267 ANGLE = 105.4149 DIHED = 388.5136
1-4 NB = 150.2071 1-4 EEL = -362.6349 VDWAALS = 10315.2635
EELEC = -73592.8205 EHBOND = 0.0000 RESTRAINT = 0.0000
*Ewald error estimate: 0.1498E-03*
------------------------------------------------------------------------------
NSTEP = 250 TIME(PS) = 0.500 TEMP(K) = 147.30 PRESS = 0.0
Etot = -48541.7164 EKtot = 4265.9580 EPtot = -52807.6743
BOND = 69.7238 ANGLE = 182.3242 DIHED = 410.9361
1-4 NB = 156.9793 1-4 EEL = -359.3038 VDWAALS = 8719.9761
EELEC = -62039.3375 EHBOND = 0.0000 RESTRAINT = 51.0274
EAMBER (non-restraint) = -52858.7018
*Ewald error estimate: 0.1365E-03*
------------------------------------------------------------------------------
Whether this error is nigligible or have any serious damage is thier. So
please tell me what is going on wrong.
Thanks and great regards
from
Navanath Kumbhar
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Received on Mon Jun 07 2010 - 03:00:04 PDT
