[gmx-users] Umbrella sampling along PCA eigenvector using make_edi

Kutzner, Carsten ckutzne at gwdg.de
Thu Mar 31 10:18:23 CEST 2016

Dear Hendrik,

that indeed looks a bit strange. If you provide the necessary input
files for a test, I could have a look at what might be wrong.
You can put them somewhere for download or email them directly
to me (not to the list, they will not be accepted).


> On 30 Mar 2016, at 16:11, Hendrik Goeddeke <hendrik.goeddeke at rub.de> wrote:
> Hi everyone,
> I want to do umbrella sampling along a PCA eigenvector using 'gmx
> make_edi'. The eigenvectors of the protein backbone atoms were computed
> using 'gmx covar'. The command for generating the 'sam.edi' file looks
> like the following:
> gmx make_edi -s topol.tpr -f eigenvec.trr -eig eigenval.xvg -restrain
> yes -harmonic yes -ori window1_backbone.gro -flood 1 -tau 0 -Eflnull 1000
> The file 'window1_backbone.gro' just contains the backbone atoms of a
> snapshot called 'window1.gro', which was used for generating
> 'topol.tpr'. I changed the eigenvalue of the first eigenvector in
> 'eigenval.xvg' to 1 to get a force constant of 1000 kJ/(mol*nm^2). When
> I then start 'gmx mdrun -ei sam.edi' the output states that the initial
> RMSD from the reference structure is not zero:
> ...
> ED: Flooding 1 eigenvector.
> ED: Initial RMSD from reference after fit = 0.371082 nm
> ...
> But when I compute the RMSD to the reference structure ('topol.tpr')
> manually by using 'gmx rms', the RMSD is zero as expected. This excludes
> a possibly wrong PBC representaion of the ED group (backbone atoms). I
> looked at the code ('edsam.c') but it seems that the RMSD is also
> computed from 'topol.tpr', which was specified in 'gmx make_edi'. I
> repeated the procedure many times but could not find any mistake.
> Any help is highly appreciated.
> Thank you very much in advance!
> All the best,
> Hendrik
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