These runs are not usable, something is unstable. There isn't really a
simple answer, it will depend on your system, the atom masks used, and the
initial structures. I would look at the output files for those middle
replicates and see which energy terms become large first. Also look at the
trajectory files - it is possible that the initial path generated from
using only endpoints became trapped on a path with a large barrier. You
can't always generate a good initial path just from the endpoints. Overall,
NEB is not really an automated tool and may take significant work to get it
running smoothly for a new system.
On Wed, Jun 6, 2018 at 12:41 AM, Aravind Ravichandran <raravind.ibab.ac.in>
wrote:
> Dear Amber Users,
> I am performing NEB having open and close forms of the protein as the end
> points. I had performed minimization on the structures and started
> heating the file as described in the tutorial
> (http://ambermd.org/tutorials/advanced/tutorial5_amber11/section4.htm).
>
> This was my input-
> Alanine NEB initial MD with small K
> &cntrl
> imin = 0, irest = 0,
> ntc=1, ntf=1,
> ntpr=1000, ntwx=1000,
> ntb = 0, cut = 999.0, rgbmax=999.0,
> igb = 1, saltcon=0.2,
> nstlim = 80000, nscm=0,
> dt = 0.0005, ig=-1,
> ntt = 3, gamma_ln=1000.0,
> tempi=0.0, temp0=300.0,
> tgtfitmask=":77-222.CA,N,C",
> tgtrmsmask=":1-70.CA,N,C",
> ineb = 1,skmin = 10,skmax = 10,
> nmropt=1,
> /
> &wt type='TEMP0', istep1=0,istep2=70000,
> value1=0.0, value2=300.0
> /
> &wt type='END'
> /
>
> I created 32 replicas, with the first 16 using copies of the
> str1.inpcrd(open) and the second 16 using copies of the
> str2.inpcrd(close).
>
> I had the following values in input file-
>
> NEB replicate breakdown:
> Energy for replicate 1 = -7948.5700
> Energy for replicate 2 = -4794.8407
> Energy for replicate 3 = -4802.4589
> Energy for replicate 4 = -4782.0042
> Energy for replicate 5 = -4851.8885
> Energy for replicate 6 = -4648.3221
> Energy for replicate 7 = -4574.8053
> Energy for replicate 8 = -4340.0242
> Energy for replicate 9 = -3886.3826
> Energy for replicate 10 = -3598.1682
> Energy for replicate 11 = -3078.5674
> Energy for replicate 12 = -2894.6292
> Energy for replicate 13 = -2538.0334
> Energy for replicate 14 = -2289.5568
> Energy for replicate 15 = 439.5811
> Energy for replicate 16 = NaN
> Energy for replicate 17 = NaN
> Energy for replicate 18 = 53846.6821
> Energy for replicate 19 = 2683.6924
> Energy for replicate 20 = -1703.6992
> Energy for replicate 21 = -2834.8332
> Energy for replicate 22 = -3560.3560
> Energy for replicate 23 = -3806.8150
> Energy for replicate 24 = -4266.6744
> Energy for replicate 25 = -4554.9216
> Energy for replicate 26 = -4702.1741
> Energy for replicate 27 = -4909.6870
> Energy for replicate 28 = -4867.9026
> Energy for replicate 29 = -4854.1495
> Energy for replicate 30 = -4844.1450
> Energy for replicate 31 = -4926.5483
> Energy for replicate 32 = -7999.0321
> Total Energy of replicates = NaN
>
>
> Whys is there a NaN in the output file. Is it okay to have it?
> How to correct it ?
>
>
> Thank you,
> Aravind R
>
>
>
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Received on Wed Jun 06 2018 - 05:30:04 PDT
