[gmx-users] a question on the -sed, trjconv output & g_order

[priyanka srivastava]

Dear Gromacs Users,

I have a doubt related to the .gro file that I am
extracting using:

trjconv -f test.trr -o test.gro -b 0 -e 1000 -sep -s
test.tpr

I get the time pattern, a portion of which is like
this in the files say from 0 to 1000ps:

h 48 lipids and 1437 waters t=  85.00001
h 48 lipids and 1437 waters t=  90.00001
h 48 lipids and 1437 waters t=  95.00001
h 48 lipids and 1437 waters t= 100.00001
h 48 lipids and 1437 waters t= 105.00001
h 48 lipids and 1437 waters t= 110.00001
h 48 lipids and 1437 waters t= 115.00001
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
h 48 lipids and 1437 waters t= 920.00006
h 48 lipids and 1437 waters t= 925.00006
h 48 lipids and 1437 waters t= 930.00006
h 48 lipids and 1437 waters t= 935.00006
h 48 lipids and 1437 waters t= 940.00006
h 48 lipids and 1437 waters t= 945.00006

My doubt is: what are these 1 and 6 in some of the
time values. I am saving the coordinates after every
5ps, why is this not exact, e.g. t= 945.00000 ?

I am facing some problem in the g_order analysis tool
of gromacs version 3.3 which might be because of the
above-mentioned problem.

When I use -b 0 -e 1000 in the g_order then it gives
me 10 frames less each time, or in other words 50ps
missing each time. 

When I run g_order for the same file in gromacs
version3.2 then it reports exactly 200 frames and
1000ps time. 

I do not think that mixing the two versions would be a
good idea, i.e. generating the trr on v3.3 and
analysing them on v3.2.

Any help would be really useful as I have trr files
but I am unable to do the analysis. 

Can this be due to some problem in the mdp file or
submitting of the run too?

kindly help,
Pri... 


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