[gmx-users] PROBLEM : rdf O-H of water from tutorial

David van der Spoel spoel at xray.bmc.uu.se
Mon Aug 11 09:08:15 CEST 2008

On Sun, 10 Aug 2008, niharendu choudhury wrote:

>Dear all,
>I tried to calculate oxygen-hydrogen (O-H) rdf of SPC water from the
>trajectory file, which I generated according to the instructions given in
>the (web)  tutorial on water. For O-H rdf i have generated the index file
>for oxygens and hydrogens. Then I calculated rdf with
>g_rdf -n
>command. When it prompted for groups,  I have chosen 1 and 2 for oxygen
>and hydrogen respectively. I have got an O-H rdf, but with an unusually
>large peak at around 0.1 nm. Also the height of this peak gets changed by
>changing the bin size. I feel it is normalization error. At 0.1 nm there
>should not be any peak due to excluded volume effect.
>If anybody clears me why this unrealistic peak is appearing? How to get
>rid of this?

you should read g_rdf -h.
you can fix this by passing a tpr file to g_rdf.

>Dr. Niharendu Choudhury
>Theoretical Chemistry Section
>Chemistry Group
>Bhabha Atomic Res. ctr.
>Mumbai 400 085, India
>Ph # 91-22-2559-2675
>Mumbai- 400 094
>Tel # 91-22-2552-7832

David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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