AW: coordinates in namd

From: Norman Geist (
Date: Tue Jun 03 2014 - 01:40:14 CDT



you could for example load the DCD to VMD and save the desired frame as PDB to use with “coordinates”. You could do the same the “catdcd” tool. But notice that you can’t also reconstruct velocities. So to be fair with both the structures you might want to re-equilibrate both of them.


Norman Geist.


Von: [] Im Auftrag von Research Jubilant
Gesendet: Dienstag, 3. Juni 2014 06:35
An: list
Betreff: namd-l: coordinates in namd


Hello everyone,

I have a 200 ns long trajectory and would like to pick two (100ns and 200ns) conformations and start simulations from each of them. While I use the restart options in namd, I don't have any problem starting from 200ns (other words, it is just continuing). But when I tried with 100ns, I am not sure how to include the coordinates. When I used 100ns.pdb in 'coordinates' option my restart files override this option. I don't have a set of restart files for 100ns conformation.

Help me with this.



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