[gmx-users] Is there any bug in gromacs v3.3 g_order analysis tool?

[priyanka srivastava]

Dear Prof. Spoel,

Many thanks for your prompt reply. It has solved my
problem.
But I have a doubt, if that is the case then everytime
it should report 5 frames missing only, why then in
some cases it reports 10 frames missing while in
others 50 missing frames?

regards,
Priyanka.

--- David van der Spoel <spoel at xray.bmc.uu.se> wrote:

> priyanka srivastava wrote:
> > Dear gromacs users,
> > 
> > I am doing a lipid-bilayer simulation using
> gromacs
> > 3.3 version. While calculating the order
> parameters,
> > although I am having a hard time.
> > 
> > When I issue the following command:
> > 
> > g_order -f lb.trr -s lb.tpr -n sn2.ndx -b 0 -e 30
> > 
> > I get the following output:
> > 
> > trn version: GMX_trn_file (single precision)
> > Reading frame       0 time    0.000   
> > Reading frame       5 time   25.000
> > 
> > i.e. 5 frames are missing.
> > 
> > If, I change -e to 40 then I get the correct
> results:
> > 
> > trn version: GMX_trn_file (single precision)
> > Reading frame       0 time    0.000   
> > Last frame          8 time   40.000
> > 
> > Also, if I issue g_order with -b 0, -e 100, output
> is:
> > 
> > trn version: GMX_trn_file (single precision)
> > Reading frame       0 time    0.000   
> > Reading frame      10 time   50.000
> > 
> > i.e. 10 frames are missing.
> > 
> > But if I change -e from 100 to 105 then
> surprisingly
> > agin I get the correct result:
> > 
> > trn version: GMX_trn_file (single precision)
> > Reading frame       0 time    0.000   
> > Last frame         20 time  100.000
> > 
> > Is there any problem with the -b, -e flags or am I
> > doing something wrong somewhere?  Has anyone ever
> > encountered a similar kind of problem?
> > 
> 
> check your output (xvg) file to see what you got.
> you may need to add .001 to the times in case of
> round-off errors.
> 
> > 
> > Kindly suggest me something,
> > eagerly waiting for the reply,
> > Pri...
> > 
> > __________________________________________________
> > Do You Yahoo!?
> > Tired of spam?  Yahoo! Mail has the best spam
> protection around 
> > http://mail.yahoo.com 
> > _______________________________________________
> > 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.
> > Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> 
> 
> -- 
> 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
> spoel at xray.bmc.uu.se	spoel at gromacs.org  
> http://folding.bmc.uu.se
>
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> 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.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
> 


__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com