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

Yuhua Song yhsong at ccb.wustl.edu
Mon Mar 15 18:10:01 CET 2004

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,


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