pkmukher wrote:
Hello users,
I am trying to check wether my prepared system is ready to
be put into a simualtion. I have a 2 body system 1protein +
1peptide. I have prepared the peptide using PRODRG server
and included it into the protein .top file. I wanted to do a
dummy minimization run with my prepared protein using 1step
of CG. I am noticing that the protein portion (not the
peptide/ligand) undergoes a shift in the X coordinate only
between the input and output structures. All of the X
coordinates are shifted by 40.37 units.
e.g. 1 -18.608 to 21.767. I have used an mdp file from a
tutorial.
following is the .mdp file and excerpts from the input and
output structure files. Could you please give me your
suggestions as to what is possibly happening here.Thanks in
advance..Prasenjit
There's no problem here. If you're not using periodic boundary
conditions
(http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions), then
energy is translation-invariant and this phenomenon doesn't matter. If
you are using periodic boundary conditions, energy is still
translation-invariant and so this doesn't matter, and what's actually
happening is GROMACS is putting the system in a simulation cell that's
convenient for it. Your X and Y coordinates happened to suit it already.
Perhaps doing some background reading on molecular dynamics simulations
is in order for you?
Mark
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