[gmx-users] Gromacs 3.3 & g_order

[priyanka srivastava]

Dear All,

Sorry for bothering you all, I was doing some mistake
while doing cat, it is working fine.

sorry for the botheration,
Pri...

--- priyanka srivastava <priyankaps4 at yahoo.com> wrote:

> Dear All,
> 
> I did a simulation of a lipid bilayer upto 10ns and
> want to calculate its order parameter using g_order
> analysis tools. Since it was restarted in the middle
> so after the completion of 10ns I used cat command
> to
> combine the trr and tpr files to make one trr and
> tpr
> files for 10ns.
> Also, by mistake I did not save the xtc file because
> I
> forgot to give the corresponding flag in the .mdp
> file.
> Now, when I issue the following command:
> 
> g_order -f test.trr -n sn2.ndx -s test.tpr -b 0 -e
> 1000
> 
> it reports:
> 
> Reading frame       0 time    0.000   Number of
> elements in first group: 48
> Reading frame     190 time  950.000
> 
> i.e. 10 frames or 50 ps less than what I specify.
> If I change -e 1000 to 1005 then it looks fine:
> 
> Reading frame       0 time    0.000   Number of
> elements in first group: 48
> Last frame        200 time 1000.000
> 
> I am a little confused. Kindly tell me what is going
> on here. I hope this is not because of of not saving
> the xtc and hence not using it for g_order analysis.
> Also, I tried using xtc file by using the trjconv
> and
> then running the same command but again the same
> error
> came up!
> Also, when I run this command for complete 10ns trr
> file (the one that I have made using cat), i.e.
> using
> -b 0 -e 10000, i get something like this:
> 
> Reading frame       0 time    0.000   Number of
> elements in first group: 48
> Last frame       2003 time 10000.000
> 
> Here 2003 frames is not clear to me. It should be
> 2000
> only if I am not wrong.
> 
> Kindly suggest me something.
> waiting eagerly for the reply,
> Pri...
> 
> 
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