I'm trying to perform MD simulation of protein-ligand complex. The step5_production.inp was set for 100ns. After running for around 30ns the program stop automatically. How will i modify the file so that the simulation restart from where it was stop. The last line from my output log file read as
"WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 13000000
WRITING COORDINATES TO DCD FILE step5_production.dcd AT STEP 13000000
WRITING COORDINATES TO RESTART FILE AT STEP 13000000
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 13000000
FINISHED WRITING RESTART VELOCITIES
LDB: ============= START OF LOAD BALANCING ============== 204045
LDB: ============== END OF LOAD BALANCING =============== 204045
Info: useSync: 0 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 204045
LDB: ============= START OF LOAD BALANCING ============== 204047
LDB: TIME 204047 LOAD: AVG 0.347167 MAX 0.364001 PROXIES: TOTAL 83 MAXPE 15 MAXPATCH 4 None MEM: 704.516 MB
LDB: TIME 204047 LOAD: AVG 0.347167 MAX 0.364001 PROXIES: TOTAL 83 MAXPE 15 MAXPATCH 4 RefineTorusLB MEM: 704.516 MB
LDB: TIME 204047 LOAD: AVG 0.347167 MAX 0.364001 PROXIES: TOTAL 83 MAXPE 15 MAXPATCH 4 RefineTorusLB MEM: 704.516 MB
LDB: ============== END OF LOAD BALANCING =============== 204047
Info: useSync: 0 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 204047"
Any recommendation will be highly helpful
You can just add the following to your script and change the first time step accordingly.
set inputname output.restart [put output name corresponding to your output]
bincoordinates output.restart.coor
binvelocities output.restart.vel
extendedSystem output.restart.xsc
firsttimestep x [put in the last timestep you obtained from your logfile]
numsteps y [put the last timestep you hope to achieve]
Make sure the firsttimestep in your initial script which read 0 is hashed out so that it utilizes the new firsttimestep you added from your previous run.
Also hash out the temperature in the restart script (not the set temperature). It would look something like this depending on how you formulated your simulation script.
# -------Temperature control----
set temperature z [write temperature set by you in the previous run]
#temperature $temperature; # initial temperature
Hash out any minimization or reinitvels that you might have added in the initial script.
This is all you need to restart the simulation from the last timestep recorded. Don't forget to record the logs and the outputs for the same under different names. Otherwise, your previous results might get overwritten. Hope this helps!
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