Klauda Lab Simulation Wiki

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====== Backup Data Instructions ======


Contained in this wiki are instructions for backing your data on the **Klauda Lab Backup Server**. The name of this server is //klauda-bkup1.umd.edu// and can only be reached on computers on the UMD network.  Your UMD password/userid is needed to log into this server. You'll need to logon to ZT1 first if you need to access this server outside campus without VPN.

==== Policies ====

If you have simulation data, then it **MUST** be backed up in two places in the event of failure of hardware. Data is categorized as either being published or unpublished. As you start in the lab your work is in progress for publication but essential for a potential future publication. Published data is after you've had your work accepted by a scientific journal and no longer requires more simulation or analysis.

// Unpublished Data //

This will be the data you are currently running simulations and analysis on. This will be automatically backed up on a daily basis. If you are a new user (after 7/1/2023), please let Dr. Klauda know so he can add you to the list of users to backup data.  If you run on ACCESS resources, this data needs to be copied to ZT1 for data analysis and backups.

// Published Data //

Once you have data that is published, you need to reduce the trajectory file sizes and make a single tarred and compressed file (.tar.gz). The name of this file should make it clear to me what publication this is from and be placed in your backup directory on the backup server. Then you will create another backup on an external hard drive (see Dr. Klauda) and remove data from ZT1.  So you still have two locations (external HD and backup server). The DCD/trajectory files should be reduced to save space. If you have 100-400ns of data, then reduce this to have only 10ps frames. If longer, consult with Dr. Klauda on the frame rate. 

==== File Reduction Instructions ====

Download the following directory to reduce dcd files. It is adapted from recenter script from EDP analysis. Adjust crystal parameters in ''cryst.str'' and file range in ''recenter1.inp''. Also change the "skip" option as needed.

{{ ::truncate.tar.gz |}}

When ready, mv the files into the dcd directory, which will overwrite the large dcd files.