[gmx-users] lipid bilayer equilibriation questions

Rama Gullapalli quantrum75 at yahoo.com
Mon Sep 12 19:54:50 CEST 2005

Dear GMX ers
I have a some basic questions regarding bilayers. I
ran the equilibriation run
for a bilayer built from scratch.

The way i ran it is,Build the bilayer,scale it to get
roughly the expected area
per lipid,Run under NVT for some time, and then turn
on the NPT coupling.

When i initially scale the box, the final coordinates
are 5.8 nm by 5.9 nm in xy
for  64 lipids and thus, the system size too.

After i run the simulation, the box size remains same,
but the  system expands
to 7.4 by 7.8 in xy

1) Is this behaviour normal for an equilibriation time
of around 10 nanoseconds?

2) Now, if i want to calculate the area per lipid, how
do i go about it? Becuase
the box size is still hovering around 5.8 by 5.9, but
the system is actually
7.4 by 7.8?

3) The temperature i set for simulation to run it 323
K, but the average  temp
is 328 K in the output. Does this mean i need to
equilibriate even longer?

4) Do i need to continue equilibriating till the
system size reaches
approximately the initial box size? or do i increase
the box size for the next
run? I would then assume that the area per lipid
calculated would be thrown

5) In analysis, the density across the box, seems to
be approximately the same
values as in literature, however the average energy
and pressure are

Energy                      Average       RMSD    
Fluct.      Drift  Tot-Drift
Total Energy                -273239          0        
 0  -0.179962   -1187.75

Pressure                      Average       RMSD    
Fluct.      Drift 
Pressure (bar)              1.38778    157.862   
157.786 -0.00256371   -16.9205

How okay are these values? Are they completely off and
do i need to equilibriate

I know these are quite basic questions, but i would
highly appreciate any
guidance with the same.

Thanks again

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