[gmx-users] PCA_RMS fluctuation per residue?

라지브간디 rajiv at kaist.ac.kr
Wed May 8 10:47:16 CEST 2013

Message: 5 
Date: Wed, 8 May 2013 08:25:33 +0200 
From: Tsjerk Wassenaar <tsjerkw at gmail.com> 
Subject: Re: [gmx-users] PCA_RMS fluctuation per residue? 
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
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Thank you for the reply Tsjerk.

Could you tell me how i can visualize the motion s of eigenvectors ?  I read from somewhere, In order to reveal the 3d motions via VMD/chimera have to add the msd value in filtered pdb file of eigenvector? If that so, how it can be done?

Hi Rajiv, 

Square the values, sum them per residue and take the square root. 



On May 8, 2013 7:24 AM, "���������������" <rajiv at kaist.ac.kr> wrote: 

Dear gmx users, 

I've done covariance matrix for backbone of protein using g_covar command. 

Also, can able to plot all projections through g_anaeig. 

However, I could only able to do -rmsf: plot the RMS fluctuation per atom 
of eigenvectors BUT i wants to do them per residue? How can i achieve this? 

In manual it shows -filt: command filter the trajectory to show only the 
motion along eigenvectors. How i do visualize this kind of motions? 

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