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.
@ 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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