[gmx-users] Analyzing Desmond trajectories using GROMACS tools

[David van der Spoel]

On 06/03/17 17:53, zeineb SI CHAIB wrote:
> Dear Justin,
>
> Again, thank you very much for your fast reply, which is very clear.  However, I'm having difficulties to understand how the tools that I'll use  will not depend on the force field parameters.
>
> For example, I'll use gmx_order to compute the order parameter per atom for carbon tails. In order to run this tool, I'll need a tpr file.
> The  tpr file, by definition, will contain  the starting structure, the molecular topology and all the simulation parameters: why I have to provide a tpr file to gmx_order, if at the end the parameters that it will contain will not reallly matter?
>
> And, If I understood correctly, I can use any force field and its related POPC parameters to generate my tpr file for the analysis that I mentioned above?
>
> Many thanks for your help.
>
> Zeineb
>
>
>
>
What is needed for most analysis tools is to know where molecules start 
and end. The atoms need to match too. Then you are fine.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se