[gmx-users] Simulation of ONLY Lipid Bilayer

Anirban Ghosh reach.anirban.ghosh at gmail.com
Thu Apr 29 12:11:49 CEST 2010

On Thu, Apr 29, 2010 at 3:29 PM, Saumya <samvygupta at gmail.com> wrote:

> Hi all,
> I am using the pre-equilibriated layers from Tieleman. After the first
> energy minimization step, I removed the periodicity using trjconv. Now, in
> order to scale the lipid positions, I tried using Inflategro.
> Do I need to use strong position restraints (because that is for protein
> and I am just using the lipid bilayer)?

You want to scale the lipid positions to what? InflateGro is used to pack
the lipid molecules around a protein, but you want to simulate only lipids,
so no point in using it. If you want to simulate a lipid bilayer, you can
continue with one taken from Tieleman's site (but with what objective?).

> After the script is run, When I try doing the energy minimization, it shows
> unequal number of atoms in .gro and topology file. (the GRO Input has only
> lipid molecules where as topology files takes into account both SOL and
> lipid molecules).
How to remove this error?
InflateGro always removes all water (SOL) molecules. So you need to
resolvate the bilayer and update your .top file accordingly. Go through the
manual once.

> I am unable to find any tutorial that could guide through the steps and the
> parameters to be set while doing the simulation of only bilayers. Please
> suggest some tutorial.
> Kindly guide through the steps.
> Regards,
> Saumya
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