[gmx-users] Questions About Gromacs

[Mark Abraham]

Xi Ouyang wrote:
> 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?

Consult section 7.3 of the manual for changing the output options.

> 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?

You'll have to form this question more precisely :-)

> 3. I want to stretch the protein, how can I do this in Gromacs? Should I 
> do something with the .mdp file?

Consult the manual. You can define forces that might pull the protein 
apart in some fashion.

Mark