general question on protein-membrane simulations -complete message!

From: L. Michel Espinoza-Fonseca (
Date: Wed Apr 18 2007 - 11:38:10 CDT

Sorry, I sent a truncated message. Here is the good one :)


Hi guys,

Here I am again. I'd like to share with you my previous experiences
and I'd like to get some feedback from you. Since few months ago, I
started working on MD simulations of protein-membrane systems. It has
been a challenging task so far, and I still wonder how to solve an
issue: avoid the failure of the RATTLE algorithm.

I've been building my bilayers using the MEMBRANE. Then I minimize it
and equilibrate it for about 1 ns (first applying restraints to the
heads and finally releasing the constraints). No problem here. Then I
combine my protein and membrane, remove overlapping lipids. I minimize
and equilibrate (I only apply constraints to the heavy atoms of the
protein, allowing the lipids and water to freely move; at the end,
everything is free to move). Again, no problem here (although
sometimes I also get it). The big problem appears when I run the
actual production MD: after a couple of ns, I get the error related to
the RATTLE algorithm. Usually I just restart the simulation and I got
no problem for another 2-3 ns, let's say, and get the same error. The
interesting thing here is that when I check the atoms that are causing
the problem, there are not steric clashes or something anomalous. By
restarting the simulation, I was able to get several nanoseconds, but
at the end the RATTLE thing always appears!

So my question is: Am I missing something? I think I'm properly
equilibrating my systems, but I can't find the reasons of why I can't
get my simulation to go straight without aborting due to RATTLE

All comments are highly appreciated.


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