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

M S 18crown10 at gmail.com
Thu Jan 9 18:55:50 CET 2014

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
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
Puzzling thing is that using  same traj.trr,  beautiful g(r) for Zn-O was
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
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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