[gmx-users] RE: g_rdf

[Junfang.Zhang at csiro.au]

Hi Erik,

Thank you very much for your reply.

When I use

g_rdf -f traj.xtc -n index.ndx

to analyze the radial distribution around a specific set of particles, I
have to choose the groups manually and sometimes there is an error
message like "time limits exceeded". Can you please let me know how to
put the choices in a script file which I can submit by using command
"qsub  filename"?

Kind regards,

Jane




-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Erik Lindahl
Sent: Monday, 5 December 2005 6:33 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] RE: g_rdf

Hi Jane,

>
> I am simulating the system of water+methane. Can you please let me  
> know
> how to use g_rdf to analyze the radial distribution around a specific
> set of particles, for example, O-O O-H H-H CH4-O or CH4-CH4.

Please start by reading the manpage (or do g_rdf -h) and ask more  
specific questions if you still don't understand it. You'll need to  
create index groups for the atoms you want to analyze.

Cheers,

Erik

-----------------------------------------------------------
Erik Lindahl  <lindahl at sbc.su.se>
Assistant Professor, Stockholm Bioinformatics Center
Stockholm University, SE 106 91 Stockholm
Phone: +46 8 5537 8564     Fax: +46 8 5537 8214




_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.