Spatial distribution functions

User discussions
1

GROMACS version:5.1.4
GROMACS modification: Yes/No
Dear all,
We are calculating the spatial distribution function (SDF) of water oxygen atoms around the protein backbone hydrogen atoms and the steps which we follow are:

  1. gmx make_ndx -f a.tpr -o a.ndx
  2. gmx trjconv -f a.xtc -s a.tpr -o b.xtc -boxcenter tric -ur compact -pbc none and choose system
  3. gmx trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans and choose backnone hydrogen atoms for fit and then system
  4. gmx spatial -s a.tpr -f c.xtc -n a.ndx -bin 0.1 -nab 30
    But we little bit confusing about the 2 step that we have already apply the pbc conditions to the obtained trajectory from MD simulations MD.xtc i.e.,
    gmx trjconv -f MD.xtc -s a.tpr -pbc mol -ur compact -center -o a.xtc
    or freshly used the MD.xtc in place of a.xtc for the SDF calculation
    Kindly help me regard this
2

Hi ashkhan,

Indeed, it should be possible to plainly omit step 2 as it -pbc none does not do anything to the periodic boundary conditions.

As I see it know, we should just take step 2 off the documentation fro gmx spatial - could you check if this gives indeed the same results and reply here?