Dear Carlos
Actually, NEB is highly sensitive to KE, with 3K temperature, I am still
having about 60KCal/mol of KE now I am not sure how dependable my
calculations will be? If you think that much of residual KE is still Okk
please let me know.
Sincerely
Abhishek
On Sat, Sep 18, 2010 at 8:24 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> NEB was rewritten for Amber11 and is much more stable and has more
> features. I can advise you on using that version. I can't help with
> problems with the earlier ones, though, you'd need to see if others on
> the list know it well enough.
> is there a reason that 3K is not low enough? not much is going to
> happen between 3K and 0K.
>
>
> On Sat, Sep 18, 2010 at 8:08 PM, Abhishek Singh <asingh7.ncsu.edu> wrote:
> > 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
> >> >
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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 - 18:00:03 PDT
