[gmx-users] g_dist lifetime option

[Markus Weingarth]

Dear gromacs users,

I have a comprehension question to g_dist with the lifetime(-lt) option.

I want to determine the lifetime of a certain sidechain - ion contact (I use all ions as a group) within a radis of 0.6 nm.

output:

@    title "a_538 - K within 0.6 nm"
@    xaxis  label "Time (ps)"
@    yaxis  label "Number of contacts"
@TYPE xy
     0.000      1.183
   200.000      1.088
   400.000      1.048
   600.000      1.024
   800.000      1.000
  1000.000      0.975
  1200.000      0.958
  1400.000      0.941
  1600.000      0.924
  1800.000      0.906
  2000.000      0.888
  2200.000      0.870
  2400.000      0.851
  2600.000      0.832
  2800.000      0.812
  3000.000      0.793
  3200.000      0.773
  3400.000      0.752
etc.

I have difficulties in understanding why the number of contacts decreases to below zero, though at least one ion is constantly within a raidus of 0.6 nm. Is this a correlation function? Is it possible to look up how this is calculated here?

this says the help option :

With options -lt and -dist the number of contacts of all atoms in group 2 that are closer than a certain distance to the center of mass of group 1 are plotted as a function of the time that the contact was continously present.

Thank you very much.

Markus

  

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