Dear Friends,
I did the Simulation study for self
assembly of peptides . ( I used G96 53a6 FF )
In First Experiment, I put the two XX peptide far from each other 2.0 nm,
and run the simulation.
In the second experiment I put the two YY peptide seperated by 2.0 nm.
and run the simulation.
In nvt I used the sane parameter, but In NPT, MD simulation I run
the Parrinello-Rahman barostat with tau_P 2.0 ns for XX peptide and tau_P 1
for
YY peptide.
I found that peptide YY interaction start at 80ns and XX interaction
start at 10 ns.
I have following Question.
1>. Is it possible to compare two MD simulation which used the
same barostat but having the different tau_P ( Relaxation time).
2>. Could I make the interpretation that XX peptide start interact
more early than YY ??
3>>. Would we compare the result between the simulation that uses the
different barostat ant thermostat but still using the same Force field.
I am looking forward for reply.
With Best Wishes,
Rama David
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