Dear Carlos
Thanks a lot, I am on it
Sincerely
Abhishek
On Sat, Sep 18, 2010 at 9:16 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> in order to get the barrier energy I would definitely recommend
> umbrella sampling along the path from NEB.
>
> > Dear Carlos
> > I am studying the backbone and pathway barrier energy. I guess right now
> I
> > can start with structure calculations. But not sure how much will be
> pathway
> > barrier energy be affected.
> > Sincerely
> > Abhishek
> >
> > On Sat, Sep 18, 2010 at 8:37 PM, Carlos Simmerling <
> > carlos.simmerling.gmail.com> wrote:
> >
> >> what are you trying to learn? the change of 3K may affect energies
> >> somewhat, but the structures almost certainly won't be changing.
> >>
> >>
> >> On Sat, Sep 18, 2010 at 8:34 PM, Abhishek Singh <asingh7.ncsu.edu>
> wrote:
> >> > 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
> >> > _______________________________________________
> >> > 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 Sun Sep 19 2010 - 12:00:04 PDT
