AMBER Archive (2007)

Subject: AMBER: extracting starting structures from equilibration trajectory

From: Nikola Trbovic (nt2146_at_columbia.edu)
Date: Thu Jun 07 2007 - 13:06:15 CDT

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

EOF

 

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,

Nikola

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