[gmx-users] PMF wrong when calculating dihedral angle rotate

yujie Liu liuyujie714 at gmail.com
Sat Sep 14 04:31:03 CEST 2019

Dear gmx users,
  I want to repeat a amber tutorial
<http://ambermd.org/tutorials/advanced/tutorial17/index.htm>* by using
gromacs, which is about PMF calculation of Alanine Dipeptide Phi/Psi
 Everything is ok about the process of simulation, firstly equilibrium and
generate a series of configuration, then do long simulation respectively.
  However, When using "gmx whan -it tpr.dat -if/x pullf/x.dat -cycl"
command  to generate PMF curve, I found histo.xvg figure is very good
but profile.xvg figure is wrong. Then I check the data of profile.xvg file,
found the second column data is "-nan". I also assign -min and -max, but
still wrong.
  Finally, I found same question on the internet, the URL is
and *https://redmine.gromacs.org/issues/2609
<https://redmine.gromacs.org/issues/2609>* . At the same time, I repeat
this a sample PMF
about angle by "gmx wham", I also found "profile.xvg" is wrong.
  I use GROMACS 2019.3. I hope some expert can give me some good advice.
Whether the gromacs software can not generate correct PMF of angle?
  Thank you,
  YUjie Liu

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