On Thu, Apr 29, 2010 at 3:29 PM, Saumya <[email protected]> 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 > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > Regards, Anirban
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