Hi
I am evaluating the stability of a protein-rna complex in ethanol-water
mixture. I used the packmol program to randomly add ethanol to the box
containing water. To mimic 0.5 % EtOH concentration I added 148 Ethanols to
a box containing 77895 water molecules. I was able to minimize the system,
but the problem is it complains with MD. Both PMEMD.CUDA and Sander.MPI
failed. Sander complains that "System must be very inhomogeneous". So to
run MD in parallel versions should the system be homogeneous? Is there a
way that I can improve homogeneity?
Thank You
--
Chinthaka Nadun Ratnaweera
Mississippi State University
310 Presidents Circle
Starkville, MS 39762
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Received on Fri Jun 21 2013 - 22:00:03 PDT
