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 Tue Jun 05 2018 - 22:00:03 PDT
