[AMBER] frames in mmpbsa.py

From: Albert <mailmd2011.gmail.com>
Date: Fri, 17 Jul 2015 12:12:45 +0200


I've produced 3 round of 1 ns MD for MMPBSA calcualtion, each of then
contains 100 frames. Here is my setting:

   cut=9.0, ntb=2, ntp=1, taup=2.0,
   ntpr=5000, ntwx=5000,
   ntt=3, gamma_ln=2.0,

so if I use the following mmpbsa.in for mmpbsa.py:

    endframe=100, verbose=1,
   igb=2, saltcon=0.150
   istrng=0.150, fillratio=4.0

I am just wondering how many frames in all would be calculated? 100
frames or 300 frames? I am a little bit confused for that.

Here is my command line for mmpbsa.py:

mpirun -np 16 MMPBSA.py.MPI -O -i 06-mmpbsa.in -o
FINAL_RESULTS_MMPBSA.dat -sp sol.prmtop -cp com.prmtop -rp rec.prmtop
-lp lig.prmtop -y prod1.mdcrd prod2.mdcrd prod3.mdcrd > progress.log&

thx a lot

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Received on Fri Jul 17 2015 - 03:30:02 PDT
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