[gmx-users] RDF of Zn_water system using VMD/g_rdf

abhijit Kayal abhijitchemiitd at gmail.com
Thu Jan 9 19:07:42 CET 2014

in g_rdf command you are selecting Zn vs SOL. You first make an index file
for only water O atom. Then run g_rdf command and select group O. regarding
your second part I am not sure. Can you post the picture of msd? It will be
helpful what is going on.

On Thu, Jan 9, 2014 at 11:09 PM, M S <18crown10 at gmail.com> wrote:

> Dear friends
> A production run of 2 ns was performed for Zn2+-water system.
> Now I wanted to generate RDF of (Zn-O) and MSD of Zn ion in water.
> I followed two methods
> 1. First using
> trjconv  -f traj.trr -o trajout.gro
> then opening in vmd and got excellent g(r) for Zn-O with running
> integration number, n(r).
> But failed to generate using g_rdf command
> make_ndx -f traj.trr -s topol.tpr -o index.ndx
> here i am selecting the whole system as group
> then
> g_rdf -n index -o rdf.xvg
> when it is asking for reference group and 1 more group
> I am selecting ZN and SOL
> but when plotting using xmgrace i am geeting multiple peak , one before
> r_minimum.
> Puzzling thing is that using  same traj.trr,  beautiful g(r) for Zn-O was
> predicted.
> It will be appreciated if someone catch the fault.
> second problem (same run for 2 ns)
> g_msd -f traj.trr -s topol.tpr -o msd.xvg
> when it is asking for the group selection
> I am giving ZN
> but the msd.xvg is found to be noisy and non linear if i read it using
> xmgrace.
> Should I have to run the simulation for time than 2 ns. The system size is
> only 1 ZN and 215 water molecules.
> Thanks in advance
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Abhijit kayal
Research Scholar
Theoretical Chemistry
IIT Kanpur

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