[gmx-users] How to extract the first three PC's cosine content from the "coscont.xvg" file?
tsjerkw at gmail.com
Tue Apr 10 13:12:40 CEST 2012
A converged system will yield low cosine content. But that can't be
turned around! I can think of a lot of lines that don't match well
with a cosine, but that are inconsistent with convergence.
That said, the index in the .xvg file is the principal component
index. So the projection on the first pc has a cosine content of 0.6.
On Tue, Apr 10, 2012 at 5:28 AM, a a <patd_2 at hotmail.com> wrote:
> Dear Sir/Madam,
> I used the following steps to get the cosine content for my trajectories,
> could you please kindly tell me how to interpret the results?
> /usr/local/gromacs/bin/g_covar_d -s ../test.pdb -f test.binpos -o -v
> /usr/local/gromacs/bin/g_anaeig_d -s ../test.pdb -f test.binpos -v
> eigenvec.trr -proj
> /usr/local/gromacs/bin/g_analyze_d -f proj.xvg -cc -n 8
> In the final "coscont.xvg", I found the followings:
> # This file was created Tue Apr 10 10:59:12 2012
> # by the following command:
> # /usr/local/gromacs/bin/g_analyze_d -f proj.xvg -cc -n 8
> # g_analyze_d is p art of G R O M A C S:
> # Giant Rising Ordinary Mutants for A Clerical Setup
> @ title "Cosine content"
> @ xaxis label "set / half periods"
> @ yaxis label "cosine content"
> @TYPE xy
> 1 0.602921
> 2 0.011185
> 3 0.0659901
> 4 0.425943
> 5 0.204306
> 6 0.439315
> 7 0.0288551
> 8 0.0830944
> I read some literature quoted the first three PCs's cosine content, if
> the cosine content close to zero, the trajectory is converged.
> How can I extract the first three PCs's cosine content from the above
> "conscont.xvg" file? Please kindly help.
> Best regards,
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Tsjerk A. Wassenaar, Ph.D.
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
More information about the gromacs.org_gmx-users