[gmx-users] equilibriation questions

Ramachandra Rao Gullapalli rrg142 at psu.edu
Fri Sep 2 18:37:40 CEST 2005

Dear GMX ers
I have built a bilayer from scratch and now i am trying to equilibriate the
same. I had a few questions regarding the equilibriation process itself.

1) Do i need to start by using a NVT ensemble or an NPT right away?

2) If i need a NPT ensemble, do i use isotropic, semiisotropic or anisotropic
type of pressure coupling?

3) For an equilibriation, does it matter that i use the cutoffs method instead
of PME to deal with electrostatics?

4) I have this problem that the system which i am running seems to expand in 10
-20 picoseconds, causing a empty space to appear between the 2 leaflets of the
bilayer.  Why does this problem occur? How can i rectify it?

5) How long do i need to run an equilibriation? What are the criteria for a
successful equilibriation of a lipid bilayer?

I really would appreciate answers to these questions as i cannot progress
further without knowledge these.
Can anyone point me to a reference in bilayers which addresses these questions?


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