[gmx-users] Comparing the simulation

rama david ramadavidgroup at gmail.com
Sat Jul 20 11:27:37 CEST 2013

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
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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