[gmx-users] energy minimization of a bilayer

Ananya Debnath ananya.iisc at gmail.com
Fri Nov 23 11:13:26 CET 2007


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.

Thanks and Regards,

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