[gmx-users] RE:directed trajectories

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Mar 29 15:57:07 CEST 2010

Hi Stephan,

With 'collide in a specific way based on Docking', do you mean to pull
them together? I'm not certain that will be  protocollized easily. And
your ligands, are they  protein/peptide too, or do you have topologies
for them? If not, it is likely to become more dirty than quick.

Interesting mismatch between your signature and the name from the mail
address, btw :p



On Mon, Mar 29, 2010 at 3:20 PM, lloyd riggs <lloyd.riggs at gmx.ch> wrote:
> Dear Folks,
> I am new to posting here.  In any case, I wanted to set initial trajectories for two large macromolecules.  Basically I am using gromacs for several things, on would be simple energy calculations.  For this I wanted to take to proteins, or protein and larger ligands and set an initial trajactory for these in the solvent so that they collide in a specific way based on Docking, other things etc...as a quick and dirty type run.
> Does anyone have a really simple protocol,
> such as a) input output
>        b) input output,  etc...
> I have read several things in the manual that state this is possible, but I wanted to avoid a day of trying to get it to work, and just get it to work quickly.
> Grüsse
> Stephan Watkins
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands

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