Hi,
The Density of my system after adding
>solvateoct test TIP3PBOX 12.0
-I: Adding /opt/apps/amber14/dat/leap/prep to search path.
-I: Adding /opt/apps/amber14/dat/leap/lib to search path.
-I: Adding /opt/apps/amber14/dat/leap/parm to search path.
-I: Adding /opt/apps/amber14/dat/leap/cmd to search path.
Total mass 492852.154 amu, Density 0.849 g/cc
Added 25964 residues.
> savepdb test box12.pdb
Writing pdb file: box12.pdb
And after simulation run for 80 ns, the summary.DENSITY file shows an
average density of 0.98 which is stable but less than 1 gm/cc.
What could be the possible reason of density being less than 1. Also is the
simulation correct seeing the density?
Please guide.
Thanking in anticipation.
Regards,
M. Jones
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Received on Tue Jun 02 2015 - 05:30:03 PDT
