[gmx-users] mdrun_problem

[Mark Abraham]

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