problems of RATTLE with big systems

Date: Wed Dec 13 2006 - 12:46:22 CST

I am trying to simulate a lipid membrane with NAMD using Charmm force
field. I need a big system, so start with a small bilayer, minimize
and equilibrate it, and then I replicate this unit along x and y. I
don´t have problems with the little membrane, but with the large
system (680.000 atoms, more or less), I get a lot of RATTLE errors in
the first step of the equilibration.

-I minimize the system in 3 steps (minimization of waters,
minimization of the membrane with the lipids fixed and minimization
with all free). I have tried to do a better minimization (more steps
or putting constraints in the 3rd step, which I decreased gradually
until having the system free), but the RATTLE errors appeared again.

-I have also tried to make a membrane of this size using the membrane
creator of VMD (only with POPC), and I get the same error, so it is
not due to the replication process. It seems to be related to the size
of the system.

Has anybody had this kind of problem with big systems? Is there any
limitation of size with NAMD? I am using NAMD 2.6b1.
Thanks a lot for your help, in advance!!

Rebeca García Fandiño
Postdoctoral student
Parc Cientific de Barcelona

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