[gmx-users] genion

[Nancy Deng]

Dear All,

I used "genion" to add a Cl- to neutarlize my system. But I just noticed
that the Cl- was put within the protein. Is it supposely like this???

My understanding is that Cl- should  be in the water box but far away from
the protein to make sure not to interfere the interactions from the protein
itself.

Anything wrong???

Any suggestion would be highly appreicated.

nancy
----- Original Message ----- 
From: "Andrew Beevers" <A.J.Beevers at warwick.ac.uk>
To: <gmx-users at gromacs.org>
Sent: Monday, February 28, 2005 4:50 AM
Subject: [gmx-users] g_cluster problem


Dear all

I am trying to produce the structure with the lowest RMSD difference to the
others in the particular xtc file using g_cluster.
The problem is that the protein is in a DMPC lipid bilayer and I cannot seem
to do an RMSD comparison of just the protein structure without resulting in
a output structure which has no bilayer.

Is there any way of doing an RMSD comparison of just the protein structure
whilst including its particular lipid environment (at that time point) in
the final output structure?
Any help would be much appreciated

Thank you in advance

Dr Andy Beevers
Bioloigcal Sciences
University of Warwick
UK
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