[gmx-users] R: Md continuation with cpt

[Mark Abraham]

On 4/29/2011 6:45 PM, Anna Marabotti wrote:
>   Dear gmx-users, Mark and Justin,
> thank you for your previous and precious support, but now I have another
> doubt. As I told you previously, looking at my trajectory I can see that the
> protein is still not fully equilibrated, then I would like to continue the
> simulation. However, now if I use tpbconv with -extend and mdrun with -cpi,
> I'm forced to use the file .tpr that still contains the erroneous
> information about the init_step. On the other hand, if I make a new .tpr
> file using an .mdp file with init_step = 0, this will no longer be an exact
> continuation (at least I think so). Is there a way to manage this problem? I
> see that in tpbconv options there is the flag -nsteps, but I don't know if
> (and how) it would be a good idea to use it for this problem.

Make a new .tpr with grompp -t. See 
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations

> BTW, I tried to recover my .edr file using the command
> eneconv -e 1.edr 2.edr 3.edr 4.edr -o full.edr -settime
> as Mark suggested, and using option 0 for the first file, and "l" to set the
> time as the continuation from the end of the previous one, but it didn't
> work: I obtained a new .edr file still with the error message "timestep
> don't match", and when I transformed it into a .xvg file, there was the same
> error as previously: only few points were saved, at 0, 60, 160, 260, 5000,
> 10000 and 15000 ps (instead of 140, 200, 300 400, 5140, 10140, 15140 ps as
> previously). I don't know if I used it incorrectly. However, using the .trr
> files and the option mdrun -rerun, I obtained a new .edr file in which I
> could obtain a "coarse-grained" (the sampling was every 50000 steps) .edr
> file in which I could see that the energy values are stable. Any suggestions
> on this point?

Try to concatenate only two files, while working out how it should be 
done. Simplify, succeed, and then introduce more complexity.

See if you can use eneconv -f in.edr -o out.edr -settime (or something) 
to correct that file before attempting to concatenate in a later stage.

Mark