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

[David van der Spoel]

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...
> 
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-- 
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
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