GROMACS version: 2020.1
GROMACS modification: Yes/No
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Hi!
I’m doing a pulling simulation. I need to select the configurations for umbrella sampling, but the values of the com distance between my two proteins doesn’t make sense. First, I separated the frames of the trajectory using:
gmx trjconv -s pull.tpr -f pull.xtc -o conf.gro -sep
And I used the script on Umbrella sampling tutorial to obtain the COM distance between the two proteins in the simulation:
echo 0 | gmx trjconv -s pull.tpr -f pull.xtc -o conf.gro -sep
compute distances
for (( i=0; i<501; i++ ))
do
gmx distance -s pull.tpr -f conf${i}.gro -n index.ndx -select ‘com of group “Chain_A” plus com of group “Chain_B”’ -oall dist${i}.xvg
done
compile summary
touch summary_distances.dat
for (( i=0; i<501; i++ ))
do
d=tail -n 1 dist${i}.xvg | awk '{print $2}'
echo “{i} {d}” >> summary_distances.dat
rm dist${i}.xvg
done
exit;
The values that I got in summary_distances. dat were decreasing, like this:
0 3.815
1 3.798
2 3.889
3 3.916
4 3.915
(…)
353 3.450
354 3.398
355 3.372
356 3.294
357 3.189
358 3.184
359 3.210
360 3.085
361 3.030
362 2.964
363 2.878
364 2.858
365 2.825
366 2.738
367 2.702
368 2.670
369 2.624
(…)
395 1.411
396 1.349
397 1.287
398 1.219
399 1.232
400 1.214
401 1.145
402 1.082
403 1.083
404 1.034
405 1.006
406 0.957
407 0.952
408 0.822
409 0.829
410 0.830
411 0.855
412 0.808
And this doesn’t make sense, because the proteins clearly separate around 600ps (~ frame 440). I expected the distances to increase. Does anyone know what could be going on?