[gmx-users] PROBLEM : rdf O-H of water from tutorial
niharc2002 at yahoo.com
Mon Aug 11 08:53:00 CEST 2008
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
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?
Dr. Niharendu Choudhury
Theoretical Chemistry Section
Bhabha Atomic Res. ctr.
Mumbai 400 085, India
Ph # 91-22-2559-2675
Mumbai- 400 094
Tel # 91-22-2552-7832
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