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--- secondary_structure_vs_time [2021/11/07 19:33] – edit
+++ secondary_structure_vs_time [2021/11/07 19:53] (current) – [Steps] edit
@@ Line 10: / Line 10: @@
 ====== Steps ======
-) change the psf and dcd in ss_content.tcl according to where these files are in your directory
+  - change the psf and dcd in ss_content.tcl according to where these files are in your directory
-) change the last_file number in ss_content.csh according to the number of trajectories. If you are using a supercomputer other than deepthought2 change this file
+  - change the last_file number in ss_content.csh according to the number of trajectories. If you are using a supercomputer other than deepthought2 change this file accordingly.
-   accordingly.
+  - run ss_content.csh ( sbatch ss_content.csh)
-) run ss_content.csh ( sbatch ss_content.csh)
+  - this will give you multiple .dat files containing the secondary structure in each trajectory. you can combine these into a single secondary_structure file for further analysis.This can be done by the following code:
-) this will give you multiple .dat files containing the secondary structure in each trajectory. you can combine these into a single secondary_structure file for further analysis.
-This can be done by the following code:
+   for i in {1..40};do
+     sed '1~10!d' sec_structure-$i.dat >> ss_content.dat
+   done
+the line sed '1~10!d' in above means, we are only taking every 10th line of the secondary structure vs time.
-for i in {1..40};do
+To visualize the secondary structure you can use the Matlab file ss_content.m you need to change a few things in this file:  num_residues, num_timesteps, step-size,  and residue names at the end. You can run this file locally on you pc/mac or on the cluster
-        sed '1~10!d' sec_structure-$i.dat >> ss_content.dat
-done
+{{:sec.jpg?700|}}