[gmx-users] seperating bilayers (again)
anoddlad at yahoo.com
Fri Apr 7 00:33:50 CEST 2006
pme.c has already been patched - I've been caught out
on that previously. I tried pme_order=4 anyway, just
in case - it didn't help.
--- Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Alan Dodd wrote:
> > Hello all,
> > I've been having some trouble recently with the
> > leaflets in my bilayer gently drifting apart over
> > period of a few hundred picoseconds. Increasing
> > vdW radius hasn't helped (up to 2nm), although it
> > delay the seperation. Likewise, increasing tau_p
> > 5 up to 10. The really bizarre thing is that I've
> > been simulating peptides in bilayers using 3.2.1
> > our cluster for about 18 months now, using the
> > lipid-modified version of ffgmx and the parameters
> > listed below, and it's only since I've started
> > 3.3 on a new machine that I've had any trouble.
> > suggestions on what might be going wrong?
> > pme_order = 8
> pme_order != 4 is known to be buggy in the
> distribution version of 3.3 -
> see multiple mailing list threads. There is a fixed
> pme.c on the ftp
> site that you can find somewhere on the gromacs
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