[gmx-users] Importing a trajectory

[Latévi Max LAWSON DAKU]

Hello,

I've written a Perl script to convert my CPMD TRAJECTORY
file into a GROMACS trajectory (.gro) file.

The script is tightly bound to the studied system. But I think
that it could be quite readily used for other systems: I've
removed the specific portions of the scripts and attached
the resulting "template" to this e-mail. Hope this will be of
use to someone...


In order to use the analysis tools, a topology file is required.
I've made one (which I anyhow need in order to re-conduct
the simulation at a QM/MM level with GROMACS...).
Using these data, I've been able to use g_bond, g_angle,
and g_dist : the results are very reasonable. But when I use
g_hbond to compute h-bond or contact lifetimes, I obtain
negative values for the backward lifetime... I suspect that
the simulation time is too short to allow collecting data on
the dynamic structure of the system (~25ps, already quite
huge for a QM treatment of this system ) !?
I will investigate this further.. and will probably open a new
thread, if needed. But, in the meantime, any hint is welcomed :-)


Regards,
Max

On 20. 09. 09 17:53, Latévi Max LAWSON DAKU wrote:
> Hello,
>
> I would like to use Gromacs tools for the analysis of
> a trajectory obtained with CPMD.
>
> During the simulations, periodic boundary conditions
> have been used, but this is not reflected in the recorded
> trajectory file.
> When writing the ".gro" trajectory file, should I apply the
> periodic condition, so as to have all the atoms inside the
> simulation cell?
>
> Regards,
> Max
>
>

-- 
***********************************************
Latevi Max LAWSON DAKU
Departement de chimie physique 
Universite de Geneve - Sciences II
30, quai Ernest-Ansermet  
CH-1211 Geneve 4 
Switzerland 

Tel: (41) 22/379 6548 ++ Fax: (41) 22/379 6103
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