The .mdp settings control this entirely; mdrun command-line options do nothing here. You need to set nstxtcout > 0 to get an .xtc file and you need either nstxout, nstvout, or nstfout (depending on the level/type of output you want) for a .trr to be written.  If mdrun finds that these settings are zero, it doesn't write those trajectories.

Hi,

I am sure about the answer but you might want to check for 2 things:-

1)You are not giving wrong option, which seems unlikely since you have mentioned options for the trr and xtc. Just crosscheck though, -x option is for xtc files.Since gro file is being generated which is the last frame of your trr file, I have a strong feeling that trr files should be generated. Also, try to visualize your gro file in VMD. If that doesn't open then then there is some mistake in your previous part. 

2) Also, Check the output settings of your mdp file.

The .mdp settings control this entirely; mdrun command-line options do nothing here. You need to set nstxtcout > 0 to get an .xtc file and you need either nstxout, nstvout, or nstfout (depending on the level/type of output you want) for a .trr to be written.  If mdrun finds that these settings are zero, it doesn't write those trajectories.

Verify the line nstxtcout on your mdp file.

Dear all,

Thank you for suggesting the above points but still i have the same query because all the above mentioned options are correct in my case. i attached my .mdp file.

1-  Production .gro file is correct and open without any error.

2-  nstxtcout is 5000

one thing that i want to mention here is that when i ran the same system on Gromacs 4.6.6 it ran perfectly and generate all the files by using default command;

gmx mdrun -deffnm md_0_1

so is there some problem in version or there are some other reason?

Note that the tutorial tells you that it is for version 5.0; older versions will not work in the same way. You are using 4.5.6 (which is absolutely ancient) and the following keywords in the .mdp are not valid:

nstxout-compressed  = 5000      ; write .xtc trajectory every 10.0 ps

compressed-x-grps   = System

Those are specific to 5.0 (maybe 4.6, but that's also an outdated series). The 4.5.6 equivalents are:

nstxtcout = 5000

xtc-grps = 5000

xtc-grps = 5000

i have no group as 5000 in index file so how it can run? to check this i edited my .mdp file and ran it but it give an error

Fatal error:

Group 5000 referenced in the .mdp file was not found in the index file.

Group names must match either [moleculetype] names or custom index group

names, in which case you must supply an index file to the '-n' option

of grompp.

Sorry, typo. xtc-grps = System