[AMBER] question on section 2 of MM-PBSA tutorial

From: Andrew Voronkov <drugdesign.yandex.ru>
Date: Thu, 08 Apr 2010 11:14:17 +0400

Dear Amber users, I have question on MM-PBSA tutororial.
it is written in section 2:
"It is essential, for good results, that our system still be exploring equilibrium phase space during the production phase. We will check this in the same fashion as we did for the last equilibration step by plotting the density, temperature, total energy and backbone RMSD." What does this phrase exactly means?
Have you made here also 2 ns simulations for heating and density equilibration with weak restraints as in section 1? Or you've just made plots from production runs?
So that was done above 4 production runs?
I am not sure how much time this will take, but if I have production run of 20 nanoseconds these heating, density, constant pressure equilibrations can take quite a long time. Do I need to run them again or that was mentioned just about plotting of data from the production run? Maybe I can make them for some last parts of the system, like last 2-5 nanoseconds?
Maybe I can use production run for some of these data, but the conditions won't be the same as in the section 1.

Best regards,

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Received on Thu Apr 08 2010 - 00:30:02 PDT
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