AMBER: extracting starting structures from equilibration trajectory

From: Nikola Trbovic <>
Date: Thu, 7 Jun 2007 14:06:15 -0400

Dear all,


I'm trying to use snapshots from an NPT equilibration trajectory as starting
structures for several NVE production runs. I tried extracting snapshots as
Amber restart files from the equilibration trajectory as follows:


ptraj prmtop << EOF

trajin equi.mdcrd 300 1000 100

trajout start restart



This produces 8 restart files from the equilibration trajectory, just like I
want it to. But when I start the production runs with irest=1 and ntx=5, the
temperature starts out around 190K, although it is clearly equilibrated at
300K in the time window of the NPT equilibration trajectory that I specified
for extracting the starting structures by ptraj. How do I fix this?


Thanks a lot in advance for any suggestions,


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Received on Sun Jun 10 2007 - 06:07:25 PDT
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