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
>
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Received on Sat Sep 18 2010 - 18:30:03 PDT
