[gmx-users] Re:mdrun_problem

[Mark Abraham]

pkmukher wrote:
> Mark and other users,
> 
>   Thanks for the input. I understand that translation does
> not have any effect on the energy calculations since the
> point of reference is the protein itself.
> The problem over here is that if a translation operation is
> to be done it should perform the same operation on all the
> X,Y or Z coordinates. 

That's not necessary either... (assuming PBC) each atom can undergo an 
infinite variety of translations, each invariant modulo the box vectors, 
and energy is invariant.

>   A brief summary of the job - i have a protein + peptide
> system which i want to simulate. I have generated peptide
> itp file using PRODRG and included in the protein .top
> file. I am doing a dummy mdrun to check the system.

> I have added excerpts from the structure files and the .mdp
> file.The first is the input structure file for grompp > .trp
> file > mdrun while the second is the output of the
> mdrun.

I don't understand what you've done in these last two sentences.

> Comparing the two structures whats happening is that
> for the protein coordinates (till 1895) a tranlation is
> being performed only on the protein X coordinates while for
> the peptide the translation is being performed only on the Y
> and Z coordinates. This results in the peptide and protein
> to be placed separate from each other.Please help me with
> your suggestions. Thanks in advance

grompp will be placing both the molecules in a periodic cell convenient 
to it (with the first atom in the same cell?). We can't tell whether 
this is happening sensibly unless you provide the first few atoms of 
both molecules and the size of your cell.

You can play with trjconv (read the man page) on your output structure 
file to see what is happening here. Be aware that your visualization 
software may or may not do unexpected things to the input you give it 
when PBC effects are present.

Mark