[gmx-users] Questions About Gromacs

Xi Ouyang xouyang at uvm.edu
Thu Mar 19 04:51:51 CET 2009

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?

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.


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