[gmx-users] Questions About Gromacs

Antonia V. antonia_haha at hotmail.com
Thu Mar 19 17:34:36 CET 2009

> Date: Thu, 19 Mar 2009 11:51:51 +0800
> From: xouyang at uvm.edu
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Questions About Gromacs
> Hi, there are 3 questions I want to ask.
> 1. I run the md from the pdb file successfully and get a .trr trajectory 
> file. But when I load the .trr file in VMD, there is just 1 frame. I 
> have 1000 steps  and want to have every step as a frame. How can I do this?

You should specify in your mdp file how often you want to store data in the trr file (every how many steps)

> 2. Since I do signal processing, I want to do wavelet-based coarse 
> graining on the protein model. Then the big question is how can I 
> introduce the wavelet into gromacs?
> 3. I want to stretch the protein, how can I do this in Gromacs? Should I 
> do something with the .mdp file?
>   Thanks again.  I really look forward to someone's help.
> Xi
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