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making continuous trajectory in micellar phase solution, using gmx trjconv tool
- aelahi4
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3 years 8 months ago #8675
by aelahi4
making continuous trajectory in micellar phase solution, using gmx trjconv tool was created by aelahi4
Hi all
my simulation results contain a few micelle clusters including polymers. I have to do some msd analysis afterwards. So I need to get a continuous trajectory by removing pbc conditions using gmx trjconv tool first.
I tried different sequence of steps that I thought might solve the problem, but none worked. I included a few here:
1- try 1 (steps):
a) use gmx trjconv -pbc cluster, to find the clusters.
problem: clusters move from one side to another in different frames.
2- try 2 (steps):
following micelle clustering of manual.gromacs.org/documentation/2019.4/how-to/visualize.html
a) make a new tpr file using a structure in a frame that micelles are formed.
b) use gmx trjconv -pbc nojump
problem: structure of molecules at same frames are different from the main trajectory, polymers are separated from.
3- others:
I used multiple combinations of -pbc -fit to remove the pbc effects, none solved the problem and still micelles are loosing molecules compared to main trajectory.
I've been struggling with this issue for a few days, I highly appreciate if you could help me about this issue. Please let me know if I need to provide further
Thank you very much
my simulation results contain a few micelle clusters including polymers. I have to do some msd analysis afterwards. So I need to get a continuous trajectory by removing pbc conditions using gmx trjconv tool first.
I tried different sequence of steps that I thought might solve the problem, but none worked. I included a few here:
1- try 1 (steps):
a) use gmx trjconv -pbc cluster, to find the clusters.
problem: clusters move from one side to another in different frames.
2- try 2 (steps):
following micelle clustering of manual.gromacs.org/documentation/2019.4/how-to/visualize.html
a) make a new tpr file using a structure in a frame that micelles are formed.
b) use gmx trjconv -pbc nojump
problem: structure of molecules at same frames are different from the main trajectory, polymers are separated from.
3- others:
I used multiple combinations of -pbc -fit to remove the pbc effects, none solved the problem and still micelles are loosing molecules compared to main trajectory.
I've been struggling with this issue for a few days, I highly appreciate if you could help me about this issue. Please let me know if I need to provide further
Thank you very much
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- vainikka
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3 years 7 months ago #8684
by vainikka
Replied by vainikka on topic making continuous trajectory in micellar phase solution, using gmx trjconv tool
Hi,
Just to get this right, you have a single trajectory which contains multiple micelles, and you'd like to compute MSD for them?
You should be able to run gmx msd and use the -mol flag to make them whole.
manual.gromacs.org/archive/5.0.2/programs/gmx-msd.html
Just to get this right, you have a single trajectory which contains multiple micelles, and you'd like to compute MSD for them?
You should be able to run gmx msd and use the -mol flag to make them whole.
manual.gromacs.org/archive/5.0.2/programs/gmx-msd.html
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