RE: coordinates in namd

From: Tristan Croll (
Date: Tue Jun 03 2014 - 02:25:49 CDT

Sounds like you just need to comment out the binCoordinates line (the one that has *.restart.coor in it). If you’ve already equilibrated for 100ns you’re probably safe to leave the extendedSystem line (which defines the current size/shape of your periodic box) in place, since the box will have long since stabilized to a constant size. Just remember to put a

reinitvels $temperature

line in.

From: [] On Behalf Of Research Jubilant
Sent: Tuesday, 3 June 2014 2:35 PM
To: list
Subject: 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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