[gmx-users] periodic boundary conditions in g_rdf

[ilhan favela]

Hi Berk, thanks for the answearing.

Here is my command line:

g_rdf -f file.xtc -s file.tpr -n index.ndx -com -rdf mol_com -xy

then i select 'Protein' as reference group and 'upper-leaf_&_P8' (just the P8 atoms from the upper-leaflet) in the 1 group option.

The value of the g_rdf at the half of the box is roughly 0.5 - 0.6

In the attachment is de g(r) that i got.

Thanks in advance!
From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] periodic boundary conditions in g_rdf
Date: Mon, 3 Nov 2008 10:20:08 +0100

Hi,

To what value does your rdf go then?

You have pbc in your system, so running with -nopbc is incorrect.
The rdf will then stop at half the box, since you molecules are in the box
and your peptide is probably in the middle, leading to a longest distance
of roughly half the box.

Berk



From: ilhan_eins at live.com.mx
To: gmx-users at gromacs.org
Date: Fri, 31 Oct 2008 16:55:54 -0600
Subject: [gmx-users] periodic boundary conditions in g_rdf


Hi everybody.
I'm working a system with a peptide embedded in a lipid bilayer and I try to get the two-dimentional g_rdf for the upper leaflet around the peptide with the -xy option and periodic boundary conditions. But my RDF doesn't go to 1. When a used -nopbc i get almost the same result (just multiplied by a constant) and the RDF is always cutted at the half of size of the box.

Any help will be appreciated.

Thanks in advance.


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