[gmx-users] Usage of g_spatial

[Venkat Reddy]

Sorry for my ignorance, since the help manual uses tpr file for the first
two steps before running g_spatial, could you please tell me how I should
do them without tpr. Also when I just run g_spatial (without the first two
steps) I get the distribution of all the anions around cations, so it is
not informative.

Thank you so much for all the help


On Tue, May 7, 2013 at 2:48 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:

> I think you can process the trajectories without generating TPR.
>
> Dr. Vitaly Chaban
>
>
> On Tue, May 7, 2013 at 12:12 PM, Venkat Reddy <venkat4bt at gmail.com> wrote:
>
> > Dear gromacs users,
> >
> > I am analyzing trajectories of an ionic liquid system generated using
> AMBER
> > MD package. The force field parameters are typical of this IL system and
> > not from the existing libraries. Hence, it is difficult for me to
> generate
> > a tpr file. I understand that running the g_spatial command needs
> > pre-processing of the coordinates (Steps 1 and 2 in g_spatial help) but I
> > need tpr file for that. So there is  no way of doing g_spatial without a
> > tpr file is it? Then how do I generate tpr file for my system?
> >
> > Thanks for all the help
> > --
> > With Best Wishes
> > Venkat Reddy Chirasani
> > PhD student
> > Laboratory of Computational Biophysics
> > Department of Biotechnology
> > IIT Madras
> > Chennai
> > INDIA-600036
> > --
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036