[gmx-users] US cycl. PMF WHAM
Jens Krüger
krueger at informatik.uni-tuebingen.de
Thu Oct 27 13:51:09 CEST 2016
Hi guys,
I am trying to create some PMFs over a lipid bilayer. What I expect is
some energy barrier in the middle and flat 0 kJ/mol at either end within
the bulk water. What I obtain looks completely different (s. below).
Somehow things seem only to get accumulated ...
I tried gromacs-5.1.2 and gromacs-2016 with a plain 2x32 POPC bilayer
with explicit SPC water. A sodium ion was moved along the z-axis. The
umbrella windows were 0.16 nm apart which was enough to give a good
histogram overlap. I also tried all different pull geometries (like
direction or direction-periodic), different combinations of pull-vec
and/or pull-dim. Long story short pullx.xvg and pullf.xvg look as they
should.
Has anybody recently used wham for a cyclic simulation system like mine
and could point me in the right direction?
Thanks,
Jens
profile_cycl.xvg
# This file was created Thu Oct 27 13:17:39 2016
# Created by:
# :-) GROMACS - gmx wham, 2016 (-:
#
# Executable: /share/apps/gromacs-2016/bin/gmx
# Data prefix: /share/apps/gromacs-2016
# Working dir: /home/jk/TEST_wham/2x32bilayer
# Command line:
# gmx wham -if US_pullf.dat -it US_pulltpr.dat -cycl
# gmx wham is part of G R O M A C S:
#
# Good ROcking Metal Altar for Chronical Sinners
#
@ title "Umbrella potential"
@ xaxis label "\xx\f{} (nm)"
@ yaxis label "E (kJ mol\S-1\N)"
@TYPE xy
8.218079e+00 0.000000e+00
8.259138e+00 -1.453808e+01
8.300196e+00 -2.771650e+01
8.341254e+00 -3.957007e+01
8.382313e+00 -4.007393e+01
8.423371e+00 -4.006203e+01
8.464430e+00 -4.077983e+01
8.505488e+00 -4.273637e+01
8.546547e+00 -4.365621e+01
8.587605e+00 -4.396186e+01
8.628664e+00 -4.489658e+01
8.669722e+00 -4.695563e+01
8.710781e+00 -4.756227e+01
8.751839e+00 -4.779315e+01
8.792898e+00 -4.875336e+01
8.833956e+00 -5.061691e+01
8.875014e+00 -5.099594e+01
8.916073e+00 -5.136080e+01
8.957131e+00 -5.252051e+01
8.998190e+00 -5.423306e+01
9.039248e+00 -5.436834e+01
9.080307e+00 -5.437309e+01
9.121365e+00 -5.586618e+01
9.162424e+00 -5.806721e+01
9.203482e+00 -5.848568e+01
9.244541e+00 -5.885979e+01
9.285599e+00 -6.047803e+01
9.326658e+00 -6.212460e+01
9.367716e+00 -6.232519e+01
9.408775e+00 -6.261266e+01
9.449833e+00 -6.435541e+01
9.490891e+00 -6.601891e+01
9.531950e+00 -6.680079e+01
9.573008e+00 -6.726610e+01
9.614067e+00 -6.928643e+01
9.655125e+00 -7.040104e+01
9.696184e+00 -7.058850e+01
9.737242e+00 -7.133366e+01
9.778301e+00 -7.309721e+01
9.819359e+00 -7.385375e+01
9.860418e+00 -7.393032e+01
9.901476e+00 -7.453971e+01
9.942535e+00 -7.676129e+01
9.983593e+00 -7.792303e+01
1.002465e+01 -7.786883e+01
1.006571e+01 -7.890458e+01
1.010677e+01 -8.088480e+01
1.014783e+01 -8.156837e+01
1.018889e+01 -8.229634e+01
1.022994e+01 -8.341212e+01
1.027100e+01 -8.532453e+01
1.031206e+01 -8.550774e+01
1.035312e+01 -8.596879e+01
1.039418e+01 -8.725995e+01
1.043524e+01 -8.982704e+01
1.047629e+01 -9.141799e+01
1.051735e+01 -9.150754e+01
1.055841e+01 -9.225813e+01
1.059947e+01 -9.446509e+01
1.064053e+01 -9.499794e+01
1.068159e+01 -9.551207e+01
1.072265e+01 -9.695286e+01
1.076370e+01 -9.687736e+01
1.080476e+01 -9.521409e+01
1.084582e+01 -9.428931e+01
1.088688e+01 -9.621502e+01
1.092794e+01 -9.564906e+01
1.096900e+01 -9.462891e+01
1.101005e+01 -9.548737e+01
1.105111e+01 -9.496358e+01
1.109217e+01 -9.298083e+01
1.113323e+01 -9.103983e+01
1.117429e+01 -9.168412e+01
1.121535e+01 -9.090885e+01
1.125641e+01 -8.890215e+01
1.129746e+01 -8.485286e+01
1.133852e+01 -7.875365e+01
1.137958e+01 -7.220100e+01
1.142064e+01 -7.094751e+01
1.146170e+01 -6.823967e+01
1.150276e+01 -6.311153e+01
1.154381e+01 -5.684616e+01
1.158487e+01 -5.328502e+01
1.162593e+01 -5.548386e+01
1.166699e+01 -5.388937e+01
1.170805e+01 -5.052818e+01
1.174911e+01 -4.701304e+01
1.179017e+01 -4.177034e+01
1.183122e+01 -3.721595e+01
1.187228e+01 -3.274138e+01
1.191334e+01 -2.610395e+01
1.195440e+01 -1.932645e+01
1.199546e+01 -1.347417e+01
1.203652e+01 -5.751585e+00
1.207757e+01 3.004301e+00
1.211863e+01 1.170099e+01
1.215969e+01 1.851744e+01
1.220075e+01 1.840928e+01
1.224181e+01 1.949559e+01
1.228287e+01 2.322574e+01
1.232393e+01 2.736396e+01
1.236498e+01 3.061556e+01
1.240604e+01 3.345170e+01
1.244710e+01 3.834237e+01
1.248816e+01 4.311155e+01
1.252922e+01 4.609151e+01
1.257028e+01 4.917021e+01
1.261133e+01 5.353265e+01
1.265239e+01 5.742819e+01
1.269345e+01 6.025915e+01
1.273451e+01 6.375255e+01
1.277557e+01 6.852059e+01
1.281663e+01 7.338687e+01
1.285769e+01 7.657370e+01
1.289874e+01 7.718161e+01
1.293980e+01 7.953524e+01
1.298086e+01 8.256788e+01
1.302192e+01 8.435080e+01
1.306298e+01 8.566306e+01
1.310404e+01 8.444558e+01
1.314509e+01 8.148106e+01
1.318615e+01 8.112091e+01
1.322721e+01 8.165058e+01
1.326827e+01 8.148502e+01
1.330933e+01 7.860781e+01
1.335039e+01 7.705772e+01
1.339145e+01 7.672663e+01
1.343250e+01 7.567109e+01
1.347356e+01 7.463517e+01
1.351462e+01 7.501714e+01
1.355568e+01 7.551324e+01
1.359674e+01 7.536590e+01
1.363780e+01 7.202062e+01
1.367885e+01 6.896017e+01
1.371991e+01 6.704583e+01
1.376097e+01 6.465844e+01
1.380203e+01 6.186874e+01
1.384309e+01 6.072334e+01
1.388415e+01 6.044725e+01
1.392521e+01 5.936857e+01
1.396626e+01 5.619722e+01
1.400732e+01 5.406754e+01
1.404838e+01 5.299572e+01
1.408944e+01 5.140967e+01
1.413050e+01 5.138894e+01
1.417156e+01 5.330179e+01
1.421261e+01 5.539074e+01
1.425367e+01 5.164527e+01
1.429473e+01 4.801661e+01
1.433579e+01 4.703899e+01
1.437685e+01 4.674970e+01
1.441791e+01 4.842742e+01
1.445897e+01 4.993277e+01
1.450002e+01 5.114466e+01
1.454108e+01 5.138557e+01
1.458214e+01 4.756526e+01
1.462320e+01 4.451700e+01
1.466426e+01 4.273276e+01
1.470532e+01 4.136105e+01
1.474637e+01 3.936585e+01
1.478743e+01 3.870822e+01
1.482849e+01 3.880372e+01
1.486955e+01 3.739843e+01
1.491061e+01 3.564741e+01
1.495167e+01 3.620496e+01
1.499273e+01 3.730068e+01
1.503378e+01 3.638231e+01
1.507484e+01 3.351377e+01
1.511590e+01 3.268477e+01
1.515696e+01 3.213354e+01
1.519802e+01 3.107083e+01
1.523908e+01 3.014555e+01
1.528013e+01 2.986782e+01
1.532119e+01 2.969210e+01
1.536225e+01 2.842044e+01
1.540331e+01 2.611228e+01
1.544437e+01 2.540154e+01
1.548543e+01 2.494961e+01
1.552649e+01 2.331058e+01
1.556754e+01 2.161008e+01
1.560860e+01 2.101755e+01
1.564966e+01 2.052478e+01
1.569072e+01 1.895686e+01
1.573178e+01 1.695218e+01
1.577284e+01 1.643979e+01
1.581389e+01 1.549973e+01
1.585495e+01 1.364889e+01
1.589601e+01 1.225845e+01
1.593707e+01 1.225543e+01
1.597813e+01 1.183702e+01
1.601919e+01 9.748903e+00
1.606025e+01 8.698902e+00
1.610130e+01 8.712552e+00
1.614236e+01 7.885662e+00
1.618342e+01 5.924825e+00
1.622448e+01 5.348074e+00
1.626554e+01 5.056070e+00
1.630660e+01 4.901779e+00
1.634765e+01 4.688225e+00
1.638871e+01 3.619418e+00
profile.xvg
# This file was created Thu Oct 27 13:35:00 2016
# Created by:
# :-) GROMACS - gmx wham, 2016 (-:
#
# Executable: /share/apps/gromacs-2016/bin/gmx
# Data prefix: /share/apps/gromacs-2016
# Working dir: /home/jk/TEST_wham/2x32bilayer
# Command line:
# gmx wham -if US_pullf.dat -it US_pulltpr.dat
# gmx wham is part of G R O M A C S:
#
# GRoups of Organic Molecules in ACtion for Science
#
@ title "Umbrella potential"
@ xaxis label "\xx\f{} (nm)"
@ yaxis label "E (kJ mol\S-1\N)"
@TYPE xy
8.218079e+00 0.000000e+00
8.259138e+00 2.712823e-01
8.300196e+00 2.341981e+00
8.341254e+00 2.796633e+00
8.382313e+00 3.185920e+00
8.423371e+00 3.255993e+00
8.464430e+00 3.174290e+00
8.505488e+00 3.491998e+00
8.546547e+00 3.635705e+00
8.587605e+00 3.500438e+00
8.628664e+00 3.233488e+00
8.669722e+00 3.294659e+00
8.710781e+00 3.550293e+00
8.751839e+00 3.498403e+00
8.792898e+00 3.485602e+00
8.833956e+00 3.816967e+00
8.875014e+00 4.099343e+00
8.916073e+00 3.915707e+00
8.957131e+00 3.867491e+00
8.998190e+00 4.176775e+00
9.039248e+00 4.531218e+00
9.080307e+00 4.705089e+00
9.121365e+00 4.436978e+00
9.162424e+00 4.421086e+00
9.203482e+00 4.535635e+00
9.244541e+00 4.373111e+00
9.285599e+00 4.088497e+00
9.326658e+00 4.309293e+00
9.367716e+00 4.485420e+00
9.408775e+00 4.449548e+00
9.449833e+00 4.322126e+00
9.490891e+00 4.638338e+00
9.531950e+00 4.230170e+00
9.573008e+00 4.036925e+00
9.614067e+00 3.591659e+00
9.655125e+00 4.002860e+00
9.696184e+00 4.075891e+00
9.737242e+00 3.757704e+00
9.778301e+00 3.926372e+00
9.819359e+00 4.384750e+00
9.860418e+00 4.490325e+00
9.901476e+00 4.359887e+00
9.942535e+00 4.214316e+00
9.983593e+00 4.281294e+00
1.002465e+01 4.526418e+00
1.006571e+01 4.073450e+00
1.010677e+01 4.275533e+00
1.014783e+01 4.676815e+00
1.018889e+01 4.121654e+00
1.022994e+01 3.649004e+00
1.027100e+01 3.775235e+00
1.031206e+01 4.408691e+00
1.035312e+01 4.078564e+00
1.039418e+01 3.384076e+00
1.043524e+01 2.959387e+00
1.047629e+01 2.370577e+00
1.051735e+01 2.510229e+00
1.055841e+01 2.921891e+00
1.059947e+01 2.958010e+00
1.064053e+01 3.018949e+00
1.068159e+01 2.802259e+00
1.072265e+01 2.716051e+00
1.076370e+01 3.760854e+00
1.080476e+01 5.663113e+00
1.084582e+01 7.757925e+00
1.088688e+01 8.389544e+00
1.092794e+01 9.727112e+00
1.096900e+01 1.094986e+01
1.101005e+01 1.115567e+01
1.105111e+01 1.308126e+01
1.109217e+01 1.535628e+01
1.113323e+01 1.784100e+01
1.117429e+01 1.922780e+01
1.121535e+01 2.106214e+01
1.125641e+01 2.374107e+01
1.129746e+01 2.875848e+01
1.133852e+01 3.515483e+01
1.137958e+01 4.279561e+01
1.142064e+01 4.721879e+01
1.146170e+01 5.134071e+01
1.150276e+01 5.663924e+01
1.154381e+01 6.316060e+01
1.158487e+01 6.869938e+01
1.162593e+01 7.016461e+01
1.166699e+01 7.296556e+01
1.170805e+01 7.679426e+01
1.174911e+01 8.172169e+01
1.179017e+01 8.765354e+01
1.183122e+01 9.263401e+01
1.187228e+01 9.852806e+01
1.191334e+01 1.058597e+02
1.195440e+01 1.131171e+02
1.199546e+01 1.205630e+02
1.203652e+01 1.290216e+02
1.207757e+01 1.378609e+02
1.211863e+01 1.466823e+02
1.215969e+01 1.547520e+02
1.220075e+01 1.589975e+02
1.224181e+01 1.637691e+02
1.228287e+01 1.682649e+02
1.232393e+01 1.725659e+02
1.236498e+01 1.767497e+02
1.240604e+01 1.814030e+02
1.244710e+01 1.867531e+02
1.248816e+01 1.917534e+02
1.252922e+01 1.962425e+02
1.257028e+01 2.014334e+02
1.261133e+01 2.062278e+02
1.265239e+01 2.103266e+02
1.269345e+01 2.144394e+02
1.273451e+01 2.195270e+02
1.277557e+01 2.245811e+02
1.281663e+01 2.295994e+02
1.285769e+01 2.340767e+02
1.289874e+01 2.381315e+02
1.293980e+01 2.419596e+02
1.298086e+01 2.451516e+02
1.302192e+01 2.469613e+02
1.306298e+01 2.484780e+02
1.310404e+01 2.489370e+02
1.314509e+01 2.488408e+02
1.318615e+01 2.492212e+02
1.322721e+01 2.498986e+02
1.326827e+01 2.506325e+02
1.330933e+01 2.504692e+02
1.335039e+01 2.500599e+02
1.339145e+01 2.499566e+02
1.343250e+01 2.499062e+02
1.347356e+01 2.505820e+02
1.351462e+01 2.513483e+02
1.355568e+01 2.520136e+02
1.359674e+01 2.532408e+02
1.363780e+01 2.537908e+02
1.367885e+01 2.527528e+02
1.371991e+01 2.511100e+02
1.376097e+01 2.490210e+02
1.380203e+01 2.476527e+02
1.384309e+01 2.474340e+02
1.388415e+01 2.473522e+02
1.392521e+01 2.471948e+02
1.396626e+01 2.466447e+02
1.400732e+01 2.455459e+02
1.404838e+01 2.447857e+02
1.408944e+01 2.443898e+02
1.413050e+01 2.452327e+02
1.417156e+01 2.473204e+02
1.421261e+01 2.502236e+02
1.425367e+01 2.498260e+02
1.429473e+01 2.486592e+02
1.433579e+01 2.481662e+02
1.437685e+01 2.488311e+02
1.441791e+01 2.516756e+02
1.445897e+01 2.533808e+02
1.450002e+01 2.546609e+02
1.454108e+01 2.555396e+02
1.458214e+01 2.547947e+02
1.462320e+01 2.544023e+02
1.466426e+01 2.530806e+02
1.470532e+01 2.520383e+02
1.474637e+01 2.515705e+02
1.478743e+01 2.519473e+02
1.482849e+01 2.522478e+02
1.486955e+01 2.516555e+02
1.491061e+01 2.516555e+02
1.495167e+01 2.526907e+02
1.499273e+01 2.539975e+02
1.503378e+01 2.545719e+02
1.507484e+01 2.544968e+02
1.511590e+01 2.544356e+02
1.515696e+01 2.540965e+02
1.519802e+01 2.542539e+02
1.523908e+01 2.552111e+02
1.528013e+01 2.553331e+02
1.532119e+01 2.553348e+02
1.536225e+01 2.553471e+02
1.540331e+01 2.553382e+02
1.544437e+01 2.551964e+02
1.548543e+01 2.549432e+02
1.552649e+01 2.545728e+02
1.556754e+01 2.548513e+02
1.560860e+01 2.546898e+02
1.564966e+01 2.544284e+02
1.569072e+01 2.543680e+02
1.573178e+01 2.543765e+02
1.577284e+01 2.542641e+02
1.581389e+01 2.535827e+02
1.585495e+01 2.532349e+02
1.589601e+01 2.533354e+02
1.593707e+01 2.535918e+02
1.597813e+01 2.536248e+02
1.601919e+01 2.535660e+02
1.606025e+01 2.537961e+02
1.610130e+01 2.540076e+02
1.614236e+01 2.537277e+02
1.618342e+01 2.538691e+02
1.622448e+01 2.543573e+02
1.626554e+01 2.541799e+02
1.630660e+01 2.540340e+02
1.634765e+01 2.538211e+02
1.638871e+01 2.528624e+02
More information about the gromacs.org_gmx-users
mailing list