Dear Amber !
I tried NEB for a 20 basepair DNA ,
I have generated 30 images between the two DNA having different conformation ,
I tried hearting the system
It gave NAN error in energy values ,
I have read the earlier comments , it is said that it may be a problem due to , atom on each other
so, i have minimized the structures from the begining and I did the same 30 copies ,
this time also it gave the same error , the system has 1260 atoms ,
my input for heating is
----------------------------------
heating the system
&cntrl
imin = 0, irest = 0,
ntc=1, ntf=1,
ntpr=50, ntwx=500,
ntb = 0, cut = 999.0, rgbmax=999.0,
igb = 1, saltcon=0.2,
nstlim = 40000, nscm=0,
dt = 0.0005,
ntt = 3, gamma_ln=1000.0,
tempi=0, temp0=300,
ineb = 1,skmin = 10,skmax = 10,
nmropt=1
/
&wt type='TEMP0', istep1=0,istep2=35000,
value1=0.0, value2=300.0
/
&wt type='END'
/
-------------------------------------
THE ERROR I HAVE GOT :
Error in diagonalization routine dgeev
NSTEP = 700 TIME(PS) = 0.350 TEMP(K) = NaN PRESS = 0. Etot = NaN EKtot = NaN EPtot = NaN
BOND = NaN ANGLE = 5071176.2516 DIHED = 14201.1097
1-4 NB = NaN 1-4 EEL = NaN VDWAALS = -1466.7982
EELEC = 19434.5261 EGB = -866937.0286 RESTRAINT = 0.0000
NEB replicate breakdown:
Energy for replicate 1 = -9449.8655
Energy for replicate 2 = NaN
Energy for replicate 3 = NaN
Energy for replicate 4 = NaN
Energy for replicate 5 = NaN
Energy for replicate 6 = NaN
Energy for replicate 7 = NaN
Energy for replicate 8 = NaN
Energy for replicate 9 = NaN
Energy for replicate 10 = NaN
Energy for replicate 11 = NaN
Energy for replicate 12 = NaN
Energy for replicate 13 = NaN
Energy for replicate 14 = NaN
Energy for replicate 15 = NaN
Energy for replicate 16 = NaN
Energy for replicate 17 = NaN
Energy for replicate 18 = NaN
Energy for replicate 19 = NaN
Energy for replicate 20 = NaN
Energy for replicate 21 = NaN
Energy for replicate 22 = NaN
Energy for replicate 23 = NaN
Energy for replicate 24 = NaN
Energy for replicate 25 = NaN
Energy for replicate 26 = NaN
Energy for replicate 27 = NaN
--------------------------------------------------------
how to solve this ?
thanks in advance !
regards
balaji
the error i got is
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Received on Mon Dec 28 2009 - 07:30:02 PST
