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
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