[gmx-users] energy minimization of a bilayer

[Mark Abraham]

Ananya Debnath wrote:
> Hi,
> 
> I am a recent user of Gromacs. I tried to make initial configuration
> of a bilayer in united atom model having Btmac, Stearyl alcohol and
> water with packmol and then energy minimization with gromacs.
> Initially I made a bilayer with gromos87 forcefield, ffgmx.itp, and
> that worked fine. With same initial configuration I tried to set up
> another bilayer in different force-filed, ffCADMOL..itp. Initially the
> structure was a bilayer, but after energy minimization, all the Btmac
> molecules are going to one layer instead of forming bilayer though
> stearyl alcohol are on both the layer. And in vmd I could see in the
> .gro file the number of fragments are less than number of residues
> where both were same initially.
> 
> If someone points me the mistake I would be highly obliged.

You'd have to describe a lot better. I have no idea how to interpret 
"going to one layer instead of forming bilayer" or "stearyl alcohol are 
on both the layer". Then, "fragments" appear in your last sentence 
having not been mentioned previously.

The usual advice here is to start with a simple case. Use ffCADMOL.itp 
to set up a bilayer from just the lipid in vacuo and get that to 
miminize. Then increase the complexity. That way when problems arise, 
you have a smaller number of new things to consider as causes of those 
problems.

Mark