So, my answere now is you need the correct vector (s). Made me check myself real quick though...but the tutorial and manual explain it well.
Sorry again,
Stephan
Gesendet: Dienstag, 26. November 2013 um 07:43 Uhr
Von: "Tsjerk Wassenaar" <[email protected]>
An: "Discussion list for GROMACS users" <[email protected]>
Betreff: Re: [gmx-users] Normal Mode Analysis
Von: "Tsjerk Wassenaar" <[email protected]>
An: "Discussion list for GROMACS users" <[email protected]>
Betreff: Re: [gmx-users] Normal Mode Analysis
Hi Stephen,
You're confusing NMA with PCA.
Cheers,
Tsjerk
On Tue, Nov 26, 2013 at 6:30 AM, lloyd riggs <[email protected]> wrote:
> I don't know your energy break down, if you look at frames with g_anaeig
> using -first and -last to set your vector number(s), and then frames set to
> your time units desired, it will give you something you can look at with
> vmd or pymol. I have noticed though after the frst 4 or so vectors, it
> becomes dificult to see movement, as the enrgy break down for even larger
> proteins starts to become close to single amino acid or very small single
> atom contributions to the entire energy landscape. Thus hard to spot
> visually, as the enrgies might be only one or two high energy hydrogen
> bonds, etc...
>
> Stephan Watkins
> *Gesendet:* Montag, 25. November 2013 um 17:05 Uhr
> *Von:* "Sathish Kumar" <[email protected]>
> *An:* "Discussion list for GROMACS users" <[email protected]>
> *Betreff:* [gmx-users] Normal Mode Analysis
> Dear users,
>
> I am trying to do NMA
>
> First i did energy minimization using .mdp file with conjugate gradient
> method,
>
> Next i calculated hessian matrix by using integrator = nm
>
> Then i calculated the eigen vectors from 7 to 100 using g_nmeig
>
> to analyze eigen vectors i use the commands
>
> g_anaeig_d -s nm.tpr -f em-c.gro -v eigenvec.trr -eig eigenval.xvg -proj
> proj-ev1.xvg -extr
>
> ev1.pdb -rmsf rmsf-ev1.xvg -first 7 -last 7 -nframes 30
>
>
> by visuvalizing ev1.pdb, i did not found any motion in the protein.
>
>
> what is the mistake i have done?
>
> Is it correct procedure for doing NM analysis?
>
> How to analyze the eigen values obtained from hessian matrix?
>
>
> regards
> M.SathishKumar
> --
> Gromacs Users mailing list
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>
--
Tsjerk A. Wassenaar, Ph.D.
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You're confusing NMA with PCA.
Cheers,
Tsjerk
On Tue, Nov 26, 2013 at 6:30 AM, lloyd riggs <[email protected]> wrote:
> I don't know your energy break down, if you look at frames with g_anaeig
> using -first and -last to set your vector number(s), and then frames set to
> your time units desired, it will give you something you can look at with
> vmd or pymol. I have noticed though after the frst 4 or so vectors, it
> becomes dificult to see movement, as the enrgy break down for even larger
> proteins starts to become close to single amino acid or very small single
> atom contributions to the entire energy landscape. Thus hard to spot
> visually, as the enrgies might be only one or two high energy hydrogen
> bonds, etc...
>
> Stephan Watkins
> *Gesendet:* Montag, 25. November 2013 um 17:05 Uhr
> *Von:* "Sathish Kumar" <[email protected]>
> *An:* "Discussion list for GROMACS users" <[email protected]>
> *Betreff:* [gmx-users] Normal Mode Analysis
> Dear users,
>
> I am trying to do NMA
>
> First i did energy minimization using .mdp file with conjugate gradient
> method,
>
> Next i calculated hessian matrix by using integrator = nm
>
> Then i calculated the eigen vectors from 7 to 100 using g_nmeig
>
> to analyze eigen vectors i use the commands
>
> g_anaeig_d -s nm.tpr -f em-c.gro -v eigenvec.trr -eig eigenval.xvg -proj
> proj-ev1.xvg -extr
>
> ev1.pdb -rmsf rmsf-ev1.xvg -first 7 -last 7 -nframes 30
>
>
> by visuvalizing ev1.pdb, i did not found any motion in the protein.
>
>
> what is the mistake i have done?
>
> Is it correct procedure for doing NM analysis?
>
> How to analyze the eigen values obtained from hessian matrix?
>
>
> regards
> M.SathishKumar
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to [email protected].
> ------------------------------
> Diese E-Mail wurde aus dem Sicherheitsverbund E-Mail made in Germany
> versendet: http://www.gmx.net/e-mail-made-in-germany<http://www.gmx.net/e-mail-made-in-germany?mc=footer@[email protected]>
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to [email protected].
>
>
--
Tsjerk A. Wassenaar, Ph.D.
--
Gromacs Users mailing list
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