[gmx-users] electrostatic interactions

XAvier Periole x.periole at rug.nl
Mon May 3 18:50:37 CEST 2010

On May 3, 2010, at 6:40 PM, abdullah ahmed wrote:

> Actually I'd just like to know why both structures have such similar  
> coloumb energy values.
> If an electro-static interaction is being made in one structure and  
> not in the other then their coloumb energy values should be  
> different too, no? Wouldn't this be visible with simple energy  
> minimisation?
How different are they?

You mention you use encad with "full solvent". Does that mean you ahve  
the protein
solvated in a box of water?

If your point is only to show that in one case you have an  
electrostatic interaction and not
in the other you might just need to show that with an image! The  
energies after minimization
are not necessarily more meaningful ...

> I would prefer to not do molecular dynamics, because the structure  
> is biologically optimal in this conformation and molecular dynamics  
> may move it too much.
> Hotmail: Trusted email with Microsoft’s powerful SPAM protection.  
> Sign up now. --
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100503/6cef45fb/attachment.html>

More information about the gromacs.org_gmx-users mailing list