Dear Carlos
Sorry I missed you reply,
I used amber 9 for this calculation , however I do have amber 10 as well.
Please suggest.
Sincerely
Abhishek
On Sat, Sep 18, 2010 at 6:18 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 - 17:30:04 PDT
