[gmx-users] Re: Simulation problem with extended membrane system!

liu xin zgxjlx at gmail.com
Thu Sep 7 18:11:05 CEST 2006

Hello Chris

So you mean to do a constrained MDS to let the lipids "fill the gaps"
between the box edges and lipids, after that do a unconstrained MDS,
then we'll get a fine structure, am I right?

Thank you very much, I'll try that

Xin Liu

On 9/7/06, chris.neale at utoronto.ca <chris.neale at utoronto.ca> wrote:
> If you can't write a script, then do the minimization and equilibration with
> water frozen in the z dimension (freeze_groups = water; freeze_dim = n n y)
> or
> use constraints in the z dimension (posre.itp force constant 1000 along z
> and 0
> along x and y). This will stop it from going into the membrane. Before you
> start, sort the initial PDB according to z (you could do this in excel),
> remove
> any waters that you don't want, resort according to original order, and run
> pdb2gmx. Note that pope.pdb does have a small cluster of waters in the
> membrane.
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list