Dear All
I am trying to use nudged elastic band method (NEB) to calculate the lowest
energy path between two conformations of a ssDNA 320-atom molecule. I Have a
situation that in the cooling stage the temperature does not goes to zero K.
I tried reproducing the tutorial example and the results match. Shown below
is the input and output files. Please suggest.
Input file for cooling
&cntrl
imin = 0, irest = 1,
ntx=5,
ntc=1,
ntf=1,
ntpr=500,
ntwx=10000,
ntb = 0, cut = 999.0,
rgbmax=999.0,
igb = 1,
saltcon=0.2,
nstlim = 120000, nscm=
0,
dt =
0.001,
ntt = 3,
gamma_ln=1000.0,
temp0=300,
ineb = 1,skmin = 50,skmax =
50,
nmropt=1
&end
&wt
type='TEMP0', istep1=0,istep2=10000, value1=300.0,
value2=250.0
&end
&wt
type='TEMP0', istep1=10001,istep2=20000, value1=250.0,
value2=250.0
&end
&wt
type='TEMP0', istep1=20001,istep2=30000, value1=250.0,
value2=200.0
&end
&wt
type='TEMP0', istep1=30001,istep2=40000, value1=200.0,
value2=200.0
&end
&wt
type='TEMP0', istep1=40001,istep2=50000, value1=200.0,
value2=150.0
&end
&wt
type='TEMP0', istep1=50001,istep2=60000, value1=150.0,
value2=150.0
&end
&wt
type='TEMP0', istep1=60001,istep2=70000, value1=150.0,
value2=100.0
&end
&wt
type='TEMP0', istep1=70001,istep2=80000, value1=100.0,
value2=100.0
&end
&wt
type='TEMP0', istep1=80001,istep2=90000, value1=100.0,
value2=50.0
&end
&wt
type='TEMP0', istep1=90001,istep2=100000, value1=50.0,
value2=50.0
&end
&wt
type='TEMP0', istep1=100001,istep2=110000, value1=50.0,
value2=0.0
&end
&wt
type='TEMP0', istep1=110001,istep2=120000, value1=0.0,
value2=0.0
&end
&wt
type='END',
&end
END
END
Out file
NMR restraints: Bond = 0.000 Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 120000 TIME(PS) = 540.000 TEMP(K) = 3.07 PRESS =
0.0
Etot = -29617.5696 EKtot = 58.5870 EPtot =
-29676.1566
BOND = 466.7654 ANGLE = 1246.1179 DIHED =
4077.0432
1-4 NB = 1385.6467 1-4 EEL = 2338.4034 VDWAALS =
-3766.4853
EELEC = 5004.6676 EGB = -40428.3155 RESTRAINT =
0.0000
NEB replicate breakdown:
Energy for replicate 1 = -1238.3101
Energy for replicate 2 = -1445.8799
Energy for replicate 3 = -1503.1307
Energy for replicate 4 = -1520.5704
Energy for replicate 5 = -1528.3599
Energy for replicate 6 = -1531.3870
Energy for replicate 7 = -1528.7194
Energy for replicate 8 = -1530.2755
Energy for replicate 9 = -1521.5880
Energy for replicate 10 = -1521.8517
Energy for replicate 11 = -1527.8288
Energy for replicate 12 = -1527.7695
Energy for replicate 13 = -1528.7136
Energy for replicate 14 = -1526.3361
Energy for replicate 15 = -1522.5248
Energy for replicate 16 = -1517.0517
Energy for replicate 17 = -1508.0192
Energy for replicate 18 = -1486.3847
Energy for replicate 19 = -1424.8613
Energy for replicate 20 = -1236.5940
Total Energy of replicates = -29676.1566
NEB RMS = 7.351438
Sincerely,
Abhishek Singh
Doctoral student
Material Science and Engineering
North Carolina State University
Raleigh, NC 27695-7907
Phone # 5179272418
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Received on Thu Sep 16 2010 - 09:30:06 PDT
