[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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