AMBER Archive (2007)

Subject: AMBER: trajectory problem

From: Miguel Ferreira (tetrass_at_hotmail.com)
Date: Tue Feb 06 2007 - 22:52:25 CST

Hi all,

I am with a stupid problem. I run 1 ns simulation in 10 stages of 100 ps
each. The problem is that I choose ntpr, ntwr and ntwx to be 300. Only now I
notice that this gives a fractional number of frames per simulation, that is
166,7. So, the last frame is never written to the output files and the
trajectory files cannot be correctly concatenated. I was thinking to strip
the 166 frames of each stage and then concatenate the files. Is this correct
or is better to run another simulation? I want to use the trajectory for
mm-pbsa calculations.

Thanks in advance
Miguel

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