# 回复： Re: 回复： Re: [gmx-users] Is 2D projection in g_anaeig

David van der Spoel spoel at xray.bmc.uu.se
Mon Aug 14 08:16:36 CEST 2006

```xi zhao wrote:
> Dear sir:
> I am sorry. Can  I understand" 2D projection = Probability Distributions
> P(v1,v2) in Proteins 2005; 60:485. How to produce 3D

Don't know the paper, but such a projection can give you a probability
distribution if you histogram it.

> plot of P(v1,v2)? how can I look for transit paths from  P(v1,v2)? How
> can I calculate free enery in gromacs using P(v1,v2)?

You need three variables to make a three dimensional energy landscape.
Use g_sham for this (you can also use other variables there).

>
> */David van der Spoel <spoel at xray.bmc.uu.se>/* 写道：
>
>     xi zhao wrote:
>      > Dear sir : Can I understand" 2D projection = Component (PC)
>     Probability
>      > Distributions P(v1,v2)"? If this is a true, and how to define the
>     Pmax
>      > in detail?
>      > Thank you in advance!
>
>     you can specify the vectors you want with -v1 -v2
>
>      >
>      > */Nguyen Hoang Phuong /* 写道：
>      >
>      >
>      > > Dear gmx users,
>      > >
>      > > Does the 2D projection plot has something to do with convergence
>      > of the
>      > > trajectory? If so, what kind of shape of plot shows the
>     trajectory is
>      > > non-converged?
>      > >
>      > > Normally, I use RMSD plot to see if the trajectory tends to
>      > converge. Now
>      > > my concern is how to see whether trajectory is conserved or not
>      > based on
>      > > 2D projection analyses.
>      > >
>      > > Thanks in advance,
>      > >
>      > > Linda
>      > you can, for example, have a look at the 2D projection of the
>      > trajectory
>      > onto the first two principal components obtained from the principal
>      > component analysis. In this paper Proteins 2005; 60:485 we used this
>      > kind
>      > of map to check the convergence of the simulation obtained from a
>      > replica
>      > exchange simulation with the counterpart obtained from high
>      > temperature, normal simulation.
>      >
>      > Phuong
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>     --
>     David.
>     ________________________________________________________________________
>     David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>     Dept. of Cell and Molecular Biology, Uppsala University.
>     Husargatan 3, Box 596, 75124 Uppsala, Sweden
>     phone: 46 18 471 4205 fax: 46 18 511 755
>     spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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```