[gmx-users] Importing a trajectory

Latévi Max LAWSON DAKU Max.Lawson at unige.ch
Sun Sep 27 17:13:01 CEST 2009


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 :-)


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

Departement de chimie physique 
Universite de Geneve - Sciences II
30, quai Ernest-Ansermet  
CH-1211 Geneve 4 

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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: traj.cpmd2gro_raw.pl
Type: text/x-perl
Size: 4894 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090927/06b33135/attachment.bin>

More information about the gromacs.org_gmx-users mailing list