Hi dear all.
I am trying to analyze what happens when we put certain acid near a
membrane.
I did the simulation from tutorial 14 from ambermd.org with the same files
and the same input files and everything worked fine, but when I did
every step by myself, it did not work very well, the hydrophilic heads of
the lipids came out dispersed among the water molecules. I used the same
input files but I make my sistem directly from charmm-gui.org.
I noted that the box dimension changed. in tutorial 14 are:
{81.355 80.001 70.549}, the same of DOPC_128.inpcrd file.
but when I calculated this box in VMD these values were a little different:
{86.665 85.300 76.234}
In VMD I load prmtop and inpcrd files, and in the console I typed:
set all [atomselect top all]
measure center $all
measure minmax $all
My questions are:
1. why are they different if I put the same parameters suggested in
tutorial 14
2. if the change of this water box could be causing the simulation to
behave in this way.
3. how could I calculate well this water box.
thanks in advance for your support
Regards
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Received on Mon Dec 14 2020 - 13:30:02 PST
