How to resume the NAMD alchemical route binding energy calculations.

[shradheyagupta]

I have encountered interruptions during NAMD alchemical route binding energy calculations due to power failures, causing the job to stop. I am exploring the possibility of utilizing BFEE2 to generate files that enable the resumption of calculations from the point of interruption. Additionally, I am curious if there are specific configurations or adjustments needed in the .conf files within both the Bound and Unbound folders to facilitate the seamless continuation of the job.

[fhh2626]

You can restart the simulation using the .restart.coor, .restart.vel, .restart.xsc files. You need to know from which window the simulation restarts. Then change the runFEP ... line of the config file.

[shradheyagupta]

I changed the .conf file as suggested. On checking the fepout file of initial and after restarting the values are diffrent for the same window. is it okay?

[shradheyagupta]

Now after restarting the simulation, I have two distinct 'fepout' files. Is there a specific consideration for joining the files so to ensure accurate analysis, or is a simple 'cat' command sufficient?"

[fhh2626]

The fepout files have sections starting with #NEW FEP WINDOW: LAMBDA SET TO aaa LAMBDA2 bbb and end with #Free energy change for lambda window [ aaa bbb ] is xxxx ; net change until now is xxxx. For the abnormally interrupted simulation, the last section may be incomplete. You need to remove this section and join the two files (guaranteeing the LAMBDAs are consecutive in the merged file)