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End-to-end distance between atoms? #4441

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tractatus opened this issue Feb 15, 2024 · 2 comments
Open

End-to-end distance between atoms? #4441

tractatus opened this issue Feb 15, 2024 · 2 comments

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@tractatus
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Hi,

Completely new to OpenMM and was looking through the tutorials for a step-by-step guide to measure and output the end-to-end distance between two atoms in nanometers during the simulation.

Similar to this tutorial for GROMACS:
https://gromacstutorials.github.io/doc-sphinx/build/html/tutorials/stretchingpolymer.html

I have the following mol2 file and want to get the end-to-end distance between pos 94 and pos 67 (both nitrogen):

pegylated_bisTz_594.mol
  ChemDraw02132414372D

134147  0  0  0  0  0  0  0  0999 V2000
   -4.0634   -0.1538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0714    0.6706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6615    1.2487    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4865    1.2401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0635    0.6505    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0549   -0.1745    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4659   -0.7520    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6409   -0.7434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2565    1.9671    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6759    2.6775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  STY  1   2 SUP
M  SLB  1   2   2
M  SAL   2  4 131 132 133 134
M  SBL   2  1   8
M  SMT   2 SO3-
M  SBV   2   8   -0.4051   -0.7190
M  END
@peastman
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You can do something like this to print out the current distance:

positions = simulation.context.getState(getPositions=True).getPositions()
print(norm(positions[94]-positions[67]))

If you want to record it periodically during the simulation you might do something like

distances = []
for i in range(n):
    simulation.step(1000)
    positions = simulation.context.getState(getPositions=True).getPositions()
    distances.append(norm(positions[94]-positions[67]).value_in_unit(nanometers))

Another option is that you just record your whole trajectory to a DCD or XTC file. Then you can use a tool like MDTraj or MDAnalysis to analyze it later and extract the distances.

@tractatus
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@peastman thanks for the super quick response!

I'll play around with this over the weekend and see where I get and then post a reproducible example here for anyone else who might be interested in this for the future, and then close this issue.

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