[gmx-users] Simulation of ONLY Lipid Bilayer

[Anirban Ghosh]

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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Regards,

Anirban
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