[gmx-users] Problems for restarting a job after 10ns run

[tamara-frembgenkesner at uiowa.edu]

Try using the split command, with -b to specify file size:

split -b (filesize) *.trr junk

Use the last junk file (they will be labelled junkaa, junkab, etc.) to restart 
with.

Tam

Quoting Yuhua Song <yhsong at ccb.wustl.edu>:

> Dear Gromacs Colleagues:
> 
> After 10 ns run, I got a 3.2 G  *.trr file, I want to restart the run for
> another 10ns, I met the following problems:
> 
> 1) if I use "tpbconv" , it needs to read the full precision trajectory files,
> but the generated *.trr file is too large, the system can not recognize this
> file. Although I write out the *.xtc file, but *.xtc file has only the
> coordinate info, not velocity info, seems not proper for the input file for
> "tpbconv" for the restart purpose
> 
> 2) if I use "grompp",  there is the -c option, it read in the Generic
> structure. My quesiton is although when I write *.gro file, I write out both
> the coordinate and velocity info, so when using -c option to read the *.gro,
> it will also read into the velocity info? For the restart purpose, I still
> need to use "-t " option to read into the starting coordinate and velocity
> info for restart purpose, right?
> 
> 3) With "grompp", the manual said: starting coodinates can be read from
> trajectory with "-t" option, but it need to read the " *.trr" file. This
> again meet the large *.trr file issue.
> 
> So, I am wondering someone can give me some suggestion about how to handle
> the restart issue after 10ns or longer runs?
> 
> Thank you very much,
> 
> Yuhua
> 
>