[gmx-users] confusion regarding tpbconv

[Mark Abraham]

Anamika Awasthi wrote:
> Dear Xavier
> 
>  Thanks for your help, after running my tpbconv I got this

Telling us the command line might be helpful!

> Reading toplogy and shit from 2ao2_tpxout.tpr
> Reading file 2ao2_tpxout.tpr, VERSION 3.3 (single precision)
> 
> READING COORDS, VELS AND BOX FROM TRAJECTORY 2ao2_tpxout.trr...
> 
> trn version: GMX_trn_file (single precision)
> Read frame   7745: step      0 time    0.000

So we've got coordinates, velocities and simulation box at this time...

> Using frame of step 0 time 0
> Opened md2.edr as single precision energy file
> Reading frame      0 time    0.000          
> 
> READ 3 PRESSURE COUPLING MU'S FROM md2.edr

... but probably pressure coupling information only at time zero. This 
is probably because you are not writing energy information at least as 
often as you are writing the above quantities. See 
http://wiki.gromacs.org/index.php/Doing_Restarts for information here.

> nsteps = 10000000, run_step = 0, current_t = 0, until = 20000
> Extending remaining runtime until 20000 ps (now 10000000 steps)
> Writing statusfile with starting step          0 and length   10000000 
> steps...
>                                  time      0.000 and length  20000.000
> 
>  here it is written that strating step is 0.
>  Sorry for asking silly questions again and again, but really I am 
> confused that it is taking step 0 from last frame of my old.trr and 
> generating new.trr file. My 7ns simulation had over before crash and I 
> want to simulate my job for 20ns.
>    So, Hope It will strat simulation from 7ns and will rum tilll 20 ns.

You can only do this and preserve your P-coupled ensemble by using all 
of the necessary information that has all been stored at the same point 
in time. Here tpbconv says the only time that this occurred was t=0.

Mark