I replied to this before but you didn't answer- did you see it?
On Fri, Sep 17, 2010 at 5:54 PM, Abhishek Singh <asingh7.ncsu.edu> wrote:
> Dear All
> I am trying to use nudged elastic band method (NEB) to calculate the lowest
> energy path between two conformations of ssDNA 320-atom molecule. I have a
> situation that in the cooling steps after simulated annealing the
> temperature of the system does not go to zero. Temperature stays around 3K
> and KE about 60-70KCal/mol. Shown below are the out puts. However with same
> inputs i can reproduce the the results of tutorial. Please suggest what is
> the reason that temperature does not go to 0.0 K.
>
> Input file
> 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
>
> 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,
> --
> 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 Sat Sep 18 2010 - 15:30:03 PDT
