[gmx-users] Simulation of ONLY Lipid Bilayer

Saumya samvygupta at gmail.com
Thu Apr 29 11:59:32 CEST 2010

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)?

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?

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.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100429/b38d815a/attachment.html>

More information about the gromacs.org_gmx-users mailing list