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Cluster with molecules jumping through PBC
- nanogod
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10 years 8 months ago #1802
by nanogod
Cluster with molecules jumping through PBC was created by nanogod
Hey MARTINI people,
I have a simulation where my molecules form a bilayer like thingy, but I have problems with the trajectory as molecules jump out of the PBC which makes it difficult to visualize for an article.
I have tried some of the following and combinations of them, but nothing helps:
- Make your molecules whole if you want them whole.
- Cluster your molecules/particles if you want them clustered.
- If you want jumps removed, extract the first frame from the trajectory to use as reference, and
then use trjconv -pbc nojump with that first frame as reference
I have also thought about translating 4 boxes and cut off the spare molecules, but translating the different boxes with the dimensions from the gromacs file seems to be abit off!
What are you guys doing when you encounter this problem, forinstance with a lipid bilayer?
Kind regards
Nanogod
I have a simulation where my molecules form a bilayer like thingy, but I have problems with the trajectory as molecules jump out of the PBC which makes it difficult to visualize for an article.
I have tried some of the following and combinations of them, but nothing helps:
- Make your molecules whole if you want them whole.
- Cluster your molecules/particles if you want them clustered.
- If you want jumps removed, extract the first frame from the trajectory to use as reference, and
then use trjconv -pbc nojump with that first frame as reference
I have also thought about translating 4 boxes and cut off the spare molecules, but translating the different boxes with the dimensions from the gromacs file seems to be abit off!
What are you guys doing when you encounter this problem, forinstance with a lipid bilayer?
Kind regards
Nanogod
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- Clement
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10 years 8 months ago #1803
by Clement
Replied by Clement on topic Cluster with molecules jumping through PBC
Here's what I think would work for your problem:
1) Removes jumps over pbc; index for output: your whole system.
$ trjconv -f <XTC (source_trajectory)> -o <XTC1> -s TPR -pbc nojump
2) Centers your "bilayer like thingy" in your box (vertically); index for centering: bilayer, index for output: your whole system.
$ trjconv -f <XTC1> -o <XTC2> -s TPR -center
3) Puts everything back in the box; index for output: your whole system.
$ trjconv -f <XTC2> -o <XTC3> -s TPR -pbc mol
Don't see any way to do it all at once! Second point is not mandatory, but could look nicer/make life easier for your pictures.
1) Removes jumps over pbc; index for output: your whole system.
$ trjconv -f <XTC (source_trajectory)> -o <XTC1> -s TPR -pbc nojump
2) Centers your "bilayer like thingy" in your box (vertically); index for centering: bilayer, index for output: your whole system.
$ trjconv -f <XTC1> -o <XTC2> -s TPR -center
3) Puts everything back in the box; index for output: your whole system.
$ trjconv -f <XTC2> -o <XTC3> -s TPR -pbc mol
Don't see any way to do it all at once! Second point is not mandatory, but could look nicer/make life easier for your pictures.
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- xavier
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10 years 8 months ago #1805
by xavier
Replied by xavier on topic Cluster with molecules jumping through PBC
It is not clear what your problem is!
The solution Clement suggests would remove the centre of mass of he system but it is not clear if that would fix your problem. You may want to explain it a bit more. Are your molecules long?
Molecules go over the PBC and get cut ... to make them whole you can use trjconv with the -pbc mol option and the molecules are placed on the side of the box corresponding to the COM position. This does not remove the jumping across the PBC. The only way you can remove the jump across the boundaries is using -pbc nojump option, but then the central box does not reflect your system as the molecules go away ...
If you think the use of 4 box would help I'd advise you to work on it ... it should work!
The solution Clement suggests would remove the centre of mass of he system but it is not clear if that would fix your problem. You may want to explain it a bit more. Are your molecules long?
Molecules go over the PBC and get cut ... to make them whole you can use trjconv with the -pbc mol option and the molecules are placed on the side of the box corresponding to the COM position. This does not remove the jumping across the PBC. The only way you can remove the jump across the boundaries is using -pbc nojump option, but then the central box does not reflect your system as the molecules go away ...
If you think the use of 4 box would help I'd advise you to work on it ... it should work!
nanogod wrote: Hey MARTINI people,
I have a simulation where my molecules form a bilayer like thingy, but I have problems with the trajectory as molecules jump out of the PBC which makes it difficult to visualize for an article.
I have tried some of the following and combinations of them, but nothing helps:
- Make your molecules whole if you want them whole.
- Cluster your molecules/particles if you want them clustered.
- If you want jumps removed, extract the first frame from the trajectory to use as reference, and
then use trjconv -pbc nojump with that first frame as reference
I have also thought about translating 4 boxes and cut off the spare molecules, but translating the different boxes with the dimensions from the gromacs file seems to be abit off!
What are you guys doing when you encounter this problem, forinstance with a lipid bilayer?
Kind regards
Nanogod
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- nanogod
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10 years 8 months ago #1813
by nanogod
Replied by nanogod on topic Cluster with molecules jumping through PBC
Thx for the repplies, I havent tried you surgestion yet Clement, but to start of I just need some illustrative pictures for an article.
I got it to work with using multible translated boxes and cutting away the excess. Seems like I hAd a pymol problem :)
I got it to work with using multible translated boxes and cutting away the excess. Seems like I hAd a pymol problem :)
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