[gmx-users] g_rdf -xy

Berk Hess gmx3 at hotmail.com
Mon May 18 11:09:32 CEST 2009


g_rdf -xy does not do what you want.
It determines rdf's using only the x and y components of the distance and averages over z.
g_rdf hangs probably because you use -nbin 100, which sets bins with a width of 100 nm
(and not 100 bins as you probably thought).
There is currently no Gromacs tools which can easily do what you want.


Date: Mon, 18 May 2009 16:12:16 +0800
From: hyxiao at mail.ipc.ac.cn
To: gmx-users at gromacs.org
Subject: [gmx-users] g_rdf -xy

Dear gmx-users,
I simulate a vapor/water/decane/vapor interface 
system. The interface is xy plane. I want to 
analysis water structure at the interface using g_rdf program 
along z axis with -xy parameter. But the calculation is 
hanged as the following:
Select a reference group and 1 group
Group     0 
(          OW) has  2508 
Group     1 
(         HW*) has  5016 
Select a group: 0
Selected 0: 'OW'
Select a group: 0

Selected 0: 'OW'
trn version: GMX_trn_file (single precision)
frame   3000 time 4100.000  
I used the following the operation
g_rdf -f  -s  -n  -bin 100 -xy  -o  
Is the runing normal? 
Please give me some suggestion. Thanks a lot!
H.Y. Xiao
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