VMD-L Mailing List

From: Jordi Cohen (jordi_at_ks.uiuc.edu)
Date: Tue Feb 01 2005 - 12:32:38 CST

Luis,

The standard way to do this would be to run 1 sim with the appropriate
fixed selection, save it, and start a second one with a different fixed
selection, based on the final coords of the previous sim. When you click
"Done", your coordinates are saved in the VMD molecule, so it is easy to
to a sim in many parts with different conditions like that.

If you want to modify the namd script, edit a copy of the
autoimd-template.namd file and specify it in the AutoIMD options. This is
the file that "autoimd.namd" is based on.

Jordi

On Mon, 31 Jan 2005, Luis Rosales wrote:

>
> Hi all!!
>
> Jordi,
>
> I am done with the tests on AutoIMD and its running fine now. (I still have to
> make a test on a remote server)
> My problem was related to my configuration files, As Jordi pointed out, the
> Namd2 proccess was crashing before vmd was able to connect to the simulation.
>
> However, I still have a couple of questions:
>
> I have tried to use the fixedatoms on/off option without success. Is possible
> to turn on/off the fixed atoms in the middle of an autoIMD script?
> (I am thinking about optimizing the whole water/protein system in the
> beggining of the autoimd run).
>
> Thanks,
>
> Luis
>