[gmx-users] PMF of ligand transport

[XAvier Periole]

Using a flexible reference to generate a PMF is certainly not a good  
idea.

More than affecting your convergence, your distance may have only little
to do with the actual position of your ion in the channel. Imagine the  
ion is
in a stable position and has to go over some energy barrier. It likely  
that the
loop will move instead of your ion ...

You might want  to change your the reaction coordinate.

On May 10, 2010, at 3:27 PM, chris.neale at utoronto.ca wrote:

> Dear Aswathy:
>
> While not technically incorrect, it will make convergence much more  
> difficult and is probably realistically incorrect given today's cpu  
> power. But then again perhaps you have some particularly important  
> reason to make that choice. In the absence of that, find some  
> atom(s) that are as static as possible.
>
> Chris.
>
> -- original message --
>
> Ok . Now I understood. I have one more doubt , as I mentioned to  
> you, I am
> using one residue in the extracellular loop as a reference point.  
> Since this
> is in the loop, do you think it can be good reference point (due to  
> th large
> fluctuatuion in the loop, will it affect the result)?
>
> -- 
> 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 thewww  
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php