Re: [gmx-users] Re: Finding centroid for a bunch of residues

Hi Vivek, > adding a little to my question, can I view the co-ordinate of an atom > by pointing at it using mouse or can I select an atom by specifying its > co-ordinate only..? > Does any of the tool in chimera, pymol, vmd is having such facility.? In VMD the coordinates of an atom you click on

Re: [gmx-users] Some Issues on Substrates/PBC

Hi Andre, > if you are not interested in the substrate dynamics, then you could > try the freeze group options (freezegrps and freezedim). I have used > these options for graphite and it worked just fine. Thanks for your reply! In addition with the 'pbc = full' options it solves all my problems w

Re: [gmx-users] Some Issues on Substrates/PBC

Hi Justin, > In addition to that, you may consider using pbc = full to get an > infinite system and potentially avoid some of those edge effects it > looks like you are seeing. I know others have used that kind of > setup with carbon nanotubes (not my area of expertise, but I've read > the discuss

[gmx-users] Some Issues on Substrates/PBC

Dear Listmembers, This post is quite lengthy because it contains several different problems that I came across during my simulations and that I cannot figure out up to now. I included some links to pictures to give you some visualization and would be glad for every suggestion or hint even to part

[gmx-users] Re: Re: Re: Re: Simulation of silicon oxide surfaces

David van der Spoel spoel at xray.bmc.uu.se wrote: > [reference to articles] Thanks for the reference to your article and that of Wensink, that looks exactly like the information I need... Best regards, Michael Hirtz -- http://www.defux.de ___

[gmx-users] Re: Re: Re: Simulation of silicon oxide surfaces

d not be stable in itself, I would suppose that one needs position restraints to keep the substrate together in such a case. Your thoughts on this would be much appreciated, Thanks, Michael >> Any comments/suggestions , anyone? >> Thanks, >>Michael >>> On Tue, Jul

[gmx-users] Re: Simulation of silicon oxide surfaces

Any comments/suggestions , anyone? Thanks, Michael > On Tue, Jul 15, 2008 at 9:37 AM, Michael Hirtz <[EMAIL PROTECTED] >> wrote: >> Hello, >> I want to set up a silicon oxide surface with varying -OH surface group >> for my simulation. Does anybody know a tool t

[gmx-users] Simulation of silicon oxide surfaces

Hello, I want to set up a silicon oxide surface with varying -OH surface group for my simulation. Does anybody know a tool that could do that or maybe even has a topology I could start on and alter manually? Thanks for any sugesstions, Michael -- http://www.defux.de _