sir
I have done two steps of minimisations.
*min1.in*
BDNA initial minimisation solvent +
ions
&cntrl
imin =
1,
maxcyc =
1000,
ncyc =
500,
ntb =
1,
ntr =
1,
cut =
10
/
Hold the complex
fixed
500.0
RES 1
20
END
END
*min2.in*
BDNA initial minimisation whole
system
&cntrl
imin =
1,
maxcyc =
5000,
ncyc =
1000,
ntb =
1,
ntr =
0,
cut =
10
/
and after this as you suggested
"Also, in my opinion there's no need to gradually bring your system up
to your target temperature using 'nmropt' and weight-changes. Just set
tempi and temp0 equal to your target temperature and let a random
velocity distribution be chosen (which is done when irest = 0).
Last, I recommend you set ig = -1 so that the random-number generator
is seeded properly, for both the initial velocity distribution and the
Langevin thermostat."
BDNA 50 ps MD with res 10 kcal/mol
restraints
&cntrl
imin =
0,
irest =
0,
ntx =
1,
ntb =
1,
cut =
10,
ntr =
1,
ntc =
2,
ntf =
2,
tempi =
300.0,
temp0 =
300.0,
ntt =
3,
gamma_ln =
1,
nstlim = 25000, dt =
0.002,
ntpr = 500, ntwx = 500, ntwr =
1000,
nmropt = 0,
ig =
-1,
/
Keep BDNA fixed with weak
restraints
10.0
RES 1
20
END
END
The programme got stopped at the beginning itself. It showed the error
NSTEP = 500 TIME(PS) = 1.000 TEMP(K) = 245.01 PRESS =
0.0
Etot = -39897.9725 EKtot = 6227.9688 EPtot =
-46125.9413
BOND = 161.3425 ANGLE = 751.0259 DIHED =
608.2930
1-4 NB = 267.8658 1-4 EEL = -5554.0864 VDWAALS =
5996.5543
EELEC = -48505.1786 EHBOND = 0.0000 RESTRAINT =
148.2422
EAMBER (non-restraint) = -46274.1835
Ewald error estimate: 0.1792E-04
------------------------------------------------------------------------------
NSTEP = 1000 TIME(PS) = 2.000 TEMP(K) = 274.13 PRESS =
0.0
Etot = -37950.8556 EKtot = 6968.2052 EPtot =
-44919.0607
BOND = 184.9061 ANGLE = 748.3211 DIHED =
641.1166
1-4 NB = 271.7571 1-4 EEL = -5544.9752 VDWAALS =
5422.4565
EELEC = -46785.0137 EHBOND = 0.0000 RESTRAINT =
142.3708
EAMBER (non-restraint) = -45061.4315
Ewald error estimate: 0.6601E-04
------------------------------------------------------------------------------
vlimit exceeded for step 1376; vmax = 69.4332
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 2 211 585 586
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
sir can you suggest an input file for this system? (modelled DNA).
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Received on Thu Sep 29 2011 - 04:30:04 PDT
