Hi everyone,
I'm trying to fold an unfolded peptide to a helix via umbrella sampling.
I've defined 21 pulling groups, the C-Alpha atoms of the peptide, and i
am restraining the distance between these groups and the COM of the
whole peptide.
After the first two steps I used g_wham to create a potential profile, I
attached it. Here, there is one coordinate z on the x-axis which must
somehow represent all 21 distances.
I would like to know the relation between this coordinate z and my 21
pulling groups.
It would be great if someone could help.
With best regards
Sabine
# This file was created Fri Mar 9 13:06:16 2012
# by the following command:
# g_wham -ix xvg-files.dat -it tpr-files.dat
#
# g_wham is part of G R O M A C S:
#
# Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
#
@ title "Umbrella potential"
@ xaxis label "z"
@ yaxis label "E (kJ mol\S-1\N)"
@TYPE xy
4.407487e-02 0.000000e+00
5.591639e-02 4.070399e-01
6.775791e-02 -2.981291e+00
7.959943e-02 -5.333508e+00
9.144096e-02 -7.409309e+00
1.032825e-01 -8.564250e+00
1.151240e-01 -1.034032e+01
1.269655e-01 -1.164605e+01
1.388070e-01 -1.286001e+01
1.506486e-01 -1.385184e+01
1.624901e-01 -1.459815e+01
1.743316e-01 -1.530307e+01
1.861731e-01 -1.578426e+01
1.980146e-01 -1.605664e+01
2.098562e-01 -1.616250e+01
2.216977e-01 -1.608948e+01
2.335392e-01 -1.593098e+01
2.453807e-01 -1.558229e+01
2.572223e-01 -1.508509e+01
2.690638e-01 -1.449146e+01
2.809053e-01 -1.369485e+01
2.927468e-01 -1.281082e+01
3.045883e-01 -1.165711e+01
3.164299e-01 -1.071678e+01
3.282714e-01 -9.923964e+00
3.401129e-01 -9.642655e+00
3.519544e-01 -1.038548e+01
3.637959e-01 -1.099925e+01
3.756375e-01 -1.189843e+01
3.874790e-01 -1.258474e+01
3.993205e-01 -1.330497e+01
4.111620e-01 -1.381902e+01
4.230036e-01 -1.421120e+01
4.348451e-01 -1.452146e+01
4.466866e-01 -1.486773e+01
4.585281e-01 -1.513537e+01
4.703696e-01 -1.547724e+01
4.822112e-01 -1.581972e+01
4.940527e-01 -1.608593e+01
5.058942e-01 -1.630412e+01
5.177357e-01 -1.648475e+01
5.295772e-01 -1.656205e+01
5.414188e-01 -1.653687e+01
5.532603e-01 -1.632003e+01
5.651018e-01 -1.598269e+01
5.769433e-01 -1.559492e+01
5.887848e-01 -1.522794e+01
6.006264e-01 -1.485388e+01
6.124679e-01 -1.438142e+01
6.243094e-01 -1.354605e+01
6.361509e-01 -1.249608e+01
6.479925e-01 -1.102316e+01
6.598340e-01 -9.149657e+00
6.716755e-01 -7.330582e+00
6.835170e-01 -6.274012e+00
6.953585e-01 -6.042568e+00
7.072001e-01 -7.020190e+00
7.190416e-01 -7.737194e+00
7.308831e-01 -8.895074e+00
7.427246e-01 -1.049692e+01
7.545661e-01 -1.182038e+01
7.664077e-01 -1.313285e+01
7.782492e-01 -1.403993e+01
7.900907e-01 -1.470428e+01
8.019322e-01 -1.530284e+01
8.137738e-01 -1.578446e+01
8.256153e-01 -1.623801e+01
8.374568e-01 -1.647271e+01
8.492983e-01 -1.657581e+01
8.611398e-01 -1.642109e+01
8.729814e-01 -1.619268e+01
8.848229e-01 -1.580464e+01
8.966644e-01 -1.509370e+01
9.085059e-01 -1.437935e+01
9.203474e-01 -1.361145e+01
9.321890e-01 -1.285160e+01
9.440305e-01 -1.233909e+01
9.558720e-01 -1.155306e+01
9.677135e-01 -1.021065e+01
9.795551e-01 -9.338516e+00
9.913966e-01 -8.976987e+00
1.003238e+00 -8.817652e+00
1.015080e+00 -9.470851e+00
1.026921e+00 -9.820667e+00
1.038763e+00 -1.006997e+01
1.050604e+00 -1.066316e+01
1.062446e+00 -1.127834e+01
1.074287e+00 -1.207208e+01
1.086129e+00 -1.292122e+01
1.097970e+00 -1.351118e+01
1.109812e+00 -1.406413e+01
1.121653e+00 -1.450123e+01
1.133495e+00 -1.484358e+01
1.145336e+00 -1.511856e+01
1.157178e+00 -1.519334e+01
1.169019e+00 -1.528418e+01
1.180861e+00 -1.534165e+01
1.192702e+00 -1.518284e+01
1.204544e+00 -1.496524e+01
1.216385e+00 -1.464793e+01
1.228227e+00 -1.414312e+01
1.240069e+00 -1.381100e+01
1.251910e+00 -1.345924e+01
1.263752e+00 -1.307143e+01
1.275593e+00 -1.279635e+01
1.287435e+00 -1.289334e+01
1.299276e+00 -1.317916e+01
1.311118e+00 -1.340666e+01
1.322959e+00 -1.370677e+01
1.334801e+00 -1.389282e+01
1.346642e+00 -1.389117e+01
1.358484e+00 -1.367797e+01
1.370325e+00 -1.319408e+01
1.382167e+00 -1.254038e+01
1.394008e+00 -1.190404e+01
1.405850e+00 -1.138717e+01
1.417691e+00 -1.133419e+01
1.429533e+00 -1.178389e+01
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1.465057e+00 -1.367189e+01
1.476899e+00 -1.400434e+01
1.488740e+00 -1.429563e+01
1.500582e+00 -1.427973e+01
1.512424e+00 -1.416497e+01
1.524265e+00 -1.409189e+01
1.536107e+00 -1.414821e+01
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1.571631e+00 -1.443660e+01
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1.595314e+00 -1.419899e+01
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1.618997e+00 -1.346299e+01
1.630839e+00 -1.317441e+01
1.642680e+00 -1.301884e+01
1.654522e+00 -1.298276e+01
1.666363e+00 -1.298124e+01
1.678205e+00 -1.307442e+01
1.690046e+00 -1.315415e+01
1.701888e+00 -1.329994e+01
1.713729e+00 -1.344973e+01
1.725571e+00 -1.373031e+01
1.737412e+00 -1.392093e+01
1.749254e+00 -1.418429e+01
1.761095e+00 -1.437995e+01
1.772937e+00 -1.447127e+01
1.784778e+00 -1.445964e+01
1.796620e+00 -1.439627e+01
1.808462e+00 -1.422118e+01
1.820303e+00 -1.404912e+01
1.832145e+00 -1.385159e+01
1.843986e+00 -1.370086e+01
1.855828e+00 -1.371861e+01
1.867669e+00 -1.368805e+01
1.879511e+00 -1.368858e+01
1.891352e+00 -1.373426e+01
1.903194e+00 -1.387878e+01
1.915035e+00 -1.388807e+01
1.926877e+00 -1.393241e+01
1.938718e+00 -1.373434e+01
1.950560e+00 -1.346892e+01
1.962401e+00 -1.315377e+01
1.974243e+00 -1.279049e+01
1.986084e+00 -1.234067e+01
1.997926e+00 -1.199886e+01
2.009767e+00 -1.161695e+01
2.021609e+00 -1.129300e+01
2.033450e+00 -1.090519e+01
2.045292e+00 -1.058554e+01
2.057133e+00 -1.032299e+01
2.068975e+00 -1.023361e+01
2.080817e+00 -1.015305e+01
2.092658e+00 -1.018564e+01
2.104500e+00 -1.015683e+01
2.116341e+00 -1.022738e+01
2.128183e+00 -1.050393e+01
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2.151866e+00 -1.072770e+01
2.163707e+00 -1.109899e+01
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2.187390e+00 -1.153550e+01
2.199232e+00 -1.169998e+01
2.211073e+00 -1.182176e+01
2.222915e+00 -1.190607e+01
2.234756e+00 -1.187866e+01
2.246598e+00 -1.188083e+01
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2.270281e+00 -1.105010e+01
2.282122e+00 -1.051859e+01
2.293964e+00 -9.884532e+00
2.305805e+00 -8.991040e+00
2.317647e+00 -7.803472e+00
2.329488e+00 -6.265275e+00
2.341330e+00 -5.773481e+00
2.353172e+00 -4.217186e+00
2.365013e+00 -2.628273e+00
2.376855e+00 -1.084827e+00
2.388696e+00 -1.047552e+00
2.400538e+00 1.613765e+00
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