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
Home:
A-12, RANJANI,
Anushaktinagar
Mumbai- 400 094
India
Tel # 91-22-2552-7832
David.
________________________________________________________________________
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list [email protected]
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
