[gmx-users] -pbc nojump

[Mark Abraham]

On 20/10/2010 9:07 PM, leila karami wrote:
>
> Hi gromacs users
>
>
> I study simulation of protein-dna interaction using gromacs. After 
> full md simulation, because of diffusion of one strand of dna to edge 
> of box, I used trjconv -f old.xtc –o new.xtc –s *.tpr -pbc nojump -ur 
> compact –center. By this way my first problem is solved.
>
> 1)Should I use new xtc file for analysis section?
>
That depends what you want to observe, and whether periodicity is 
relevant to that observation.
>
> 2)When I see new xtc file, there isn’t any water molecule in interface 
> between protein and dna(where as there were water molecules interface 
> between protein and dna, before full md simulation). I want to survey 
> water mediated hydrogen bond between protein and dna. Do –pbc nojump 
> cause to this problem?
>
Probably. Probably what you want is to center on the combined 
protein+DNA group (need to make an index group) and then put the COM of 
all residues in the box. That will mean your water region and surrounds 
of interest are contiguous.

Mark

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