[gmx-users] g_rdf -surf

Payman Pirzadeh ppirzade at ucalgary.ca
Mon Feb 13 17:45:49 CET 2012

By the way,

The g(r) = 0.05 is around 1.75 A, which sounds to be consistent with
literature, but as r increases towards 10A, instead of converging to a value
of 1, g(r) goes towards 41000. I want to return the value of g(r) to 1.


From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: February-13-12 12:24 AM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] g_rdf -surf



Thanks for your attention. A word was missing in my previous e-mail!! The
g(r) is NOT normalized.

Here was my command:


g_rdf -f traj.xtc -s topol.tpr -n reidues_atoms.ndx -o gofr  -surf  res


The index file includes atoms in the side chain exposed to the solvent:

[ SideChain_&_r_13_r_17_r_19-21_r_24 ]

144  145  146  147  148  149  150  151  152  189  190  191  192  193  194

195  196  197  198  221  222  223  224  225  226  227  228  229  230  231

232  233  234  235  236  237  238  239  240  241  242  243  244  245  246

247  248  249  250  285  286  287  288  289  290  291  292  293  294  295

296  297  298


So, I am trying to calculate the RDF of water molecules (SOL) with respect
to the surface of the residues whose side chain atoms are listed in the
index file. What I get is a small peak in the order of  0.05 the beginning,
and then, g(r) is increasing to 41000.

Sorry for inconveniences in the first iteration.





From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Mark Abraham
Sent: February-13-12 12:06 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_rdf -surf


On 13/02/2012 5:54 PM, Payman Pirzadeh wrote: 


I am trying to calculate the RDF of water next to surface of certain
residues. I used the an index file which includes the residues as the first
group, and the #12 option (SOL) in the g_rdf, and used the option '-surf
res' on the prompt.

Please supply the actual command line copied and pasted, as well as which
groups you specified and what they contain. The information above is

However, the calculated RDF rises up to 41000 in long distances. It appears
that it is normalized (as specified by the help). How can I normalize this

If it's already normalized, what do you want to do? 41000 is what quantity?


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