[gmx-users] Questions About Gromacs
Mark.Abraham at anu.edu.au
Fri Mar 20 00:54:26 CET 2009
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.
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