Michal Walczak wrote:
I only used the same *.mdp file but *.top files where different for
protein and for 3 aa peptide, so it seems that I should use different
*.mdp file. Am I wrong? How could I obtain that *.mdp input for 3 aa
peptide?
Here's an exercise. Write down what you think the general description of
the information in a .top file is, and the general description of the
information in an .mdp file is. Look at the contents of working .mdp and
.top files if you need a clue - if you don't have working examples, do
some tutorial exercises on the gromacs webpage. Read the manual for details.
By now, you'll have started to work out the answer to your above questions.
Rough answers below (scroll down)
.mdp file : values for parameters that are required to select and
properly use different algorithms in an MD simulation, and control of
output from an MD simulation
.top file : topology (i.e. bond connectivity) for a particular chemical
system
Hence it is clear than an .mdp file has more chance of being
transferable across systems than a .top file.
Mark
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