[gmx-users] Gromacs 3.3 & g_order

[priyanka srivastava]

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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