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
Received on Sat Sep 18 2010 - 17:30:05 PDT
