Re: Tabulated potential

From: Adam Skelton (mradamskelton_at_hotmail.com)
Date: Thu Jul 26 2012 - 13:30:54 CDT

I have figured out the problem. The windows binary (on cygwin) does not
work properly for this but when I tried it using the linux binary on a
linux machine, it actually worked fine.

Thanks

Adam

On 7/23/2012 5:17 PM, Adam Skelton wrote:
> I have been trying use a tabulated potential because I want to tune
> Lennard-Jones interactions between atom-type pairs rather than setting
> the parameters and for the interactions to be calculated by mixing rules.
>
>
> I have followed the manual
> http://www.ks.uiuc.edu/Research/namd/2.8/ug/node24.html#SECTION00082600000000000000
>
>
> and I have done exactly what it says to set up the table files
> My table file is
>
> 2 0.1 12
> TYPE NOT
> 0.0000000 1.00429663e+13 -1.20515628e+15
> 0.10000000 1.00429663e+13 -1.20515628e+15
> 0.20000000 2.45180877e+09 -1.47111182e+11
> 0.30000001 18889842. -7.55749120e+08
> 0.40000001 597223.75 -17937472.
> 0.50000000 40773.203 -982910.69
> 0.60000002 4492.1699 -91058.461
> 0.69999999 677.39539 -12025.513
> 0.80000001 124.51897 -2029.9758
> 0.90000004 24.891989 -403.00790
> 1.00000000 4.3739777 -86.501709
> 1.1000000 0.0000000 -17.454546
> 1.2000000 -0.77214909 -1.7711835
> 1.3000001 -0.74341667 1.4416274
> 1.4000000 -0.57575738 1.7083439
> 1.5000000 -0.42028496 1.3715211
> 1.6000000 -0.30221865 0.99952072
> 1.7000000 -0.21762435 0.70724761
> 1.8000001 -0.15799376 0.49770772
> 1.9000000 -0.11596179 0.35186610
> 2.0000000 -8.61261636e-02 0.25102282
> 2.1000001 -6.47329763e-02 0.18105048
> 2.2000000 -4.92187515e-02 0.13210227
> 2.3000000 -3.78364697e-02 9.75083262e-02
> 2.4000001 -2.93896105e-02 7.27865323e-02
> 2.5000000 -2.30517145e-02 5.49197309e-02
> 2.6000001 -1.82460211e-02 4.18633372e-02
> 2.7000000 -1.45657575e-02 3.22196595e-02
> 2.8000000 -1.17208334e-02 2.50233971e-02
> 2.9000001 -9.50216781e-03 1.96009297e-02
> 3.0000000 -7.75750307e-03 1.54772103e-02
> 3.1000001 -6.37482246e-03 1.23136872e-02
> 3.2000000 -5.27095282e-03 9.86670330e-03
> 3.3000000 -4.38355422e-03 7.95915071e-03
> 3.4000001 -3.66550870e-03 6.46111788e-03
> 3.5000000 -3.08091100e-03 5.27646672e-03
> 3.6000001 -2.60218070e-03 4.33343509e-03
> 3.7000000 -2.20798329e-03 3.57803958e-03
> 3.8000000 -1.88169396e-03 2.96934671e-03
> 3.9000001 -1.61027384e-03 2.47609639e-03
> 4.0000000 -1.38343358e-03 2.07425258e-03
> 4.0999999 -1.19300175e-03 1.74520491e-03
> 4.2000003 -1.03245245e-03 1.47445570e-03
> 4.3000002 -8.96548037e-04 1.25064654e-03
> 4.4000001 -7.81059265e-04 1.06482068e-03
> 4.5000000 -6.82556187e-04 9.09880735e-04
> 4.5999999 -5.98243496e-04 7.80171715e-04
> 4.7000003 -5.25832525e-04 6.71165180e-04
> 4.8000002 -4.63442353e-04 5.79218962e-04
> 4.9000001 -4.09518980e-04 5.01387636e-04
> 5.0000000 -3.62774619e-04 4.35280177e-04
> 5.0999999 -3.22137610e-04 3.78947268e-04
> 5.2000003 -2.86712777e-04 3.30792769e-04
> 5.3000002 -2.55750288e-04 2.89505464e-04
> 5.4000001 -2.28619101e-04 2.54003069e-04
> 5.5000000 -2.04786920e-04 2.23389623e-04
> 5.5999999 -1.83803204e-04 1.96920693e-04
> 5.7000003 -1.65285383e-04 1.73975626e-04
> 5.8000002 -1.48907959e-04 1.54035530e-04
> 5.9000001 -1.34392743e-04 1.36664836e-04
> 6.0000000 -1.21501645e-04 1.21497033e-04
> 6.0999999 -1.10030291e-04 1.08222790e-04
> 6.2000003 -9.98027172e-05 9.65802537e-05
> 6.3000002 -9.06672576e-05 8.63473178e-05
> 6.4000001 -8.24926174e-05 7.73348293e-05
> 6.5000000 -7.51650223e-05 6.93814727e-05
> 6.5999999 -6.85856503e-05 6.23492597e-05
> 6.7000003 -6.26684196e-05 5.61198685e-05
> 6.8000002 -5.73383004e-05 5.05917124e-05
> 6.9000001 -5.25296418e-05 4.56771995e-05
> 7.0000000 -4.81849456e-05 4.13007583e-05
> 7.0999999 -4.42537494e-05 3.73970179e-05
> 7.2000003 -4.06916733e-05 3.39092949e-05
> 7.3000002 -3.74596602e-05 3.07884002e-05
> 7.4000001 -3.45232038e-05 2.79914857e-05
> 7.5000000 -3.18518214e-05 2.54812021e-05
> 7.5999999 -2.94185083e-05 2.32249240e-05
> 7.7000003 -2.71993176e-05 2.11940933e-05
> 7.8000002 -2.51730053e-05 1.93636970e-05
> 7.9000001 -2.33206374e-05 1.77117472e-05
> 8.0000000 -2.16253575e-05 1.62189081e-05
> 8.1000004 -2.00721170e-05 1.48681411e-05
> 8.1999998 -1.86474972e-05 1.36444314e-05
> 8.3000002 -1.73394455e-05 1.25344704e-05
> 8.4000006 -1.61371954e-05 1.15265093e-05
> 8.5000000 -1.50310925e-05 1.06101334e-05
> 8.6000004 -1.40124293e-05 9.77607033e-06
> 8.6999998 -1.30734115e-05 9.01610929e-06
> 8.8000002 -1.22069850e-05 8.32291244e-06
> 8.9000006 -1.14068152e-05 7.68995960e-06
> 9.0000000 -1.06671805e-05 7.11143002e-06
> 9.1000004 -9.98289124e-06 6.58210502e-06
> 9.1999998 -9.34927539e-06 6.09733615e-06
> 9.3000002 -8.76208014e-06 5.65293931e-06
> 9.4000006 -8.21746289e-06 5.24517554e-06
> 9.5000000 -7.71193663e-06 4.87068519e-06
> 9.6000004 -7.24231950e-06 4.52643917e-06
> 9.6999998 -6.80573248e-06 4.20972265e-06
> 9.8000002 -6.39954033e-06 3.91807816e-06
> 9.9000006 -6.02135196e-06 3.64929724e-06
> 10.0000000 -5.66898598e-06 3.40138558e-06
> 10.100000 -5.34044057e-06 3.17253352e-06
> 10.200000 -5.03389901e-06 2.96111239e-06
> 10.300000 -4.74768740e-06 2.76563901e-06
> 10.400001 -4.48028231e-06 2.58477439e-06
> 10.500000 -4.23028632e-06 2.41730345e-06
> 10.600000 -3.99641249e-06 2.26211750e-06
> 10.700000 -3.77748734e-06 2.11821475e-06
> 10.800000 -3.57242470e-06 1.98467819e-06
> 10.900001 -3.38023256e-06 1.86067632e-06
> 11.000000 -3.19999731e-06 1.74545130e-06
> 11.100000 -3.03087336e-06 1.63830828e-06
> 11.200000 -2.87208763e-06 1.53861697e-06
> 11.300000 -2.72292118e-06 1.44579758e-06
> 11.400001 -2.58271552e-06 1.35932271e-06
> 11.500000 -2.45086153e-06 1.27870942e-06
> 11.600000 -2.32679326e-06 1.20351285e-06
> 11.700000 -2.20999209e-06 1.13332851e-06
> 11.800000 -2.09997324e-06 1.06778236e-06
> 11.900001 -1.99629153e-06 1.00653290e-06
> TYPE OCO
> 0.0000000 1.00429663e+13 -1.20515628e+15
> 0.10000000 3.70185862e+15 -1.20515628e+15
> 0.20000000 9.03772373e+11 -1.47111182e+11
> 0.30000001 6.96554854e+09 -7.55749120e+08
> 0.40000001 2.20621392e+08 -17937472.
> 0.50000000 15155850. -982910.69
> 0.60000002 1698277.1 -91058.461
> 0.69999999 266525.44 -12025.513
> 0.80000001 53453.945 -2029.9758
> 0.90000004 12902.390 -403.00790
> 1.00000000 3593.0203 -86.501709
> 1.1000000 1118.0894 -17.454546
> 1.2000000 378.73798 -1.7711835
> 1.3000001 136.34216 1.4416274
> 1.4000000 50.840591 1.7083439
> 1.5000000 18.976366 1.3715211
> 1.6000000 6.6643286 0.99952072
> 1.7000000 1.8446724 0.70724761
> 1.8000001 -1.27156500e-06 0.49770772
> 1.9000000 -0.64092636 0.35186610
> 2.0000000 -0.79683673 0.25102282
> 2.1000001 -0.76576668 0.18105048
> 2.2000000 -0.67198020 0.13210227
> 2.3000000 -0.56629920 9.75083262e-02
> 2.4000001 -0.46816680 7.27865323e-02
> 2.5000000 -0.38369808 5.49197309e-02
> 2.6000001 -0.31353426 4.18633372e-02
> 2.7000000 -0.25626922 3.22196595e-02
> 2.8000000 -0.20991740 2.50233971e-02
> 2.9000001 -0.17251445 1.96009297e-02
> 3.0000000 -0.14233348 1.54772103e-02
> 3.1000001 -0.11793526 1.23136872e-02
> 3.2000000 -9.81534496e-02 9.86670330e-03
> 3.3000000 -8.20560157e-02 7.95915071e-03
> 3.4000001 -6.89037070e-02 6.46111788e-03
> 3.5000000 -5.81120178e-02 5.27646672e-03
> 3.6000001 -4.92187329e-02 4.33343509e-03
> 3.7000000 -4.18580398e-02 3.57803958e-03
> 3.8000000 -3.57395932e-02 2.96934671e-03
> 3.9000001 -3.06322519e-02 2.47609639e-03
> 4.0000000 -2.63513979e-02 2.07425258e-03
> 4.0999999 -2.27489304e-02 1.74520491e-03
> 4.2000003 -1.97055973e-02 1.47445570e-03
> 4.3000002 -1.71250198e-02 1.25064654e-03
> 4.4000001 -1.49289202e-02 1.06482068e-03
> 4.5000000 -1.30535113e-02 9.09880735e-04
> 4.5999999 -1.14465896e-02 7.80171715e-04
> 4.7000003 -1.00652631e-02 6.71165180e-04
> 4.8000002 -8.87417514e-03 5.79218962e-04
> 4.9000001 -7.84404203e-03 5.01387636e-04
> 5.0000000 -6.95053954e-03 4.35280177e-04
> 5.0999999 -6.17338950e-03 3.78947268e-04
> 5.2000003 -5.49562322e-03 3.30792769e-04
> 5.3000002 -4.90300870e-03 2.89505464e-04
> 5.4000001 -4.38355235e-03 2.54003069e-04
> 5.5000000 -3.92712606e-03 2.23389623e-04
> 5.5999999 -3.52515001e-03 1.96920693e-04
> 5.7000003 -3.17033217e-03 1.73975626e-04
> 5.8000002 -2.85646366e-03 1.54035530e-04
> 5.9000001 -2.57823500e-03 1.36664836e-04
> 6.0000000 -2.33109901e-03 1.21497033e-04
> 6.0999999 -2.11115042e-03 1.08222790e-04
> 6.2000003 -1.91502552e-03 9.65802537e-05
> 6.3000002 -1.73982373e-03 8.63473178e-05
> 6.4000001 -1.58303336e-03 7.73348293e-05
> 6.5000000 -1.44247699e-03 6.93814727e-05
> 6.5999999 -1.31626287e-03 6.23492597e-05
> 6.7000003 -1.20274257e-03 5.61198685e-05
> 6.8000002 -1.10047951e-03 5.05917124e-05
> 6.9000001 -1.00821571e-03 4.56771995e-05
> 7.0000000 -9.24849650e-04 4.13007583e-05
> 7.0999999 -8.49414268e-04 3.73970179e-05
> 7.2000003 -7.81058974e-04 3.39092949e-05
> 7.3000002 -7.19035103e-04 3.07884002e-05
> 7.4000001 -6.62681181e-04 2.79914857e-05
> 7.5000000 -6.11412572e-04 2.54812021e-05
> 7.5999999 -5.64711692e-04 2.32249240e-05
> 7.7000003 -5.22119168e-04 2.11940933e-05
> 7.8000002 -4.83227544e-04 1.93636970e-05
> 7.9000001 -4.47673723e-04 1.77117472e-05
> 8.0000000 -4.15134360e-04 1.62189081e-05
> 8.1000004 -3.85320745e-04 1.48681411e-05
> 8.1999998 -3.57975485e-04 1.36444314e-05
> 8.3000002 -3.32867319e-04 1.25344704e-05
> 8.4000006 -3.09789728e-04 1.15265093e-05
> 8.5000000 -2.88557407e-04 1.06101334e-05
> 8.6000004 -2.69003300e-04 9.77607033e-06
> 8.6999998 -2.50977871e-04 9.01610929e-06
> 8.8000002 -2.34345731e-04 8.32291244e-06
> 8.9000006 -2.18985326e-04 7.68995960e-06
> 9.0000000 -2.04786862e-04 7.11143002e-06
> 9.1000004 -1.91650732e-04 6.58210502e-06
> 9.1999998 -1.79487281e-04 6.09733615e-06
> 9.3000002 -1.68214858e-04 5.65293931e-06
> 9.4000006 -1.57759772e-04 5.24517554e-06
> 9.5000000 -1.48055042e-04 4.87068519e-06
> 9.6000004 -1.39039621e-04 4.52643917e-06
> 9.6999998 -1.30658256e-04 4.20972265e-06
> 9.8000002 -1.22860351e-04 3.91807816e-06
> 9.9000006 -1.15600029e-04 3.64929724e-06
> 10.0000000 -1.08835397e-04 3.40138558e-06
> 10.100000 -1.02528051e-04 3.17253352e-06
> 10.200000 -9.66430962e-05 2.96111239e-06
> 10.300000 -9.11484240e-05 2.76563901e-06
> 10.400001 -8.60147848e-05 2.58477439e-06
> 10.500000 -8.12153521e-05 2.41730345e-06
> 10.600000 -7.67254169e-05 2.26211750e-06
> 10.700000 -7.25224527e-05 2.11821475e-06
> 10.800000 -6.85856212e-05 1.98467819e-06
> 10.900001 -6.48958667e-05 1.86067632e-06
> 11.000000 -6.14356541e-05 1.74545130e-06
> 11.100000 -5.81887580e-05 1.63830828e-06
> 11.200000 -5.51403318e-05 1.53861697e-06
> 11.300000 -5.22765768e-05 1.44579758e-06
> 11.400001 -4.95848471e-05 1.35932271e-06
> 11.500000 -4.70534542e-05 1.27870942e-06
> 11.600000 -4.46715349e-05 1.20351285e-06
> 11.700000 -4.24291247e-05 1.13332851e-06
> 11.800000 -4.03169252e-05 1.06778236e-06
> 11.900001 -3.83263832e-05 1.00653290e-06
>
>
> and I have put the following into my parameter file
>
> NBTABLE
> OT N NOT
> OT OC30A OCO
>
> I keep getting this error however.
>
> FATAL ERROR: ERROR: Expected 2 tabulated energy types but got 1
>
> I have clearly put in two different energy types but it seems like the
> second one isn't being read. If I just have one type (either one), it
> works fine, however. Have I got the format wrong? I have even tried
> going through the source code and can't figure out what I am doing wrong.
>
> Any help would be appreciated
>
> Thanks in advance
>
> Adam
>
>
>
>
>
>
>
>
>
>
>
>
>

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