[gmx-users] cutoffs vs pme and lipids

Xavier Periole periole at inka.mssm.edu
Thu Jan 23 02:55:25 CET 2003

Hi Lynne,

I have experienced the same pattern when I began to
run simulations of pure lipids. The only thing you
have to be sure is that your membrane is fully
equilibrated within the parameters (cutoff, PME,
pressure coupling, temperature etc ...) you use.
Specially if you 
use a membrane already equilibrated. My experience
is that the membrane can take a while to equilibrate.
No offence to Peter's membrane, they are very useful,
but if you switch to PME, you better equilibrate it
again an before putting the protein inside.

In the simulations I do now I use the semi-isotropic
control of the pressure, PME (cutoff 0.9nm), and cut
vdW at 1.2nm. The area/lipid is approximately 64 A*2
for POPC. Note that when cutting the vdW at 0.9nm I
had a area/lipid of 68A*2.

Hope it will help you.


Physiology & Biophysics Dept.
Mount Sinai School of Medicine
New York, NY 10029.

tel : 1 212 241 8192
fax : 1 212 860 3369
e-mail : periole at physbio.mssm.edu
web-site : http://physbio.mssm.edu/~periole

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