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Contact Analysis
- Imamul
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6 years 1 month ago - 6 years 1 month ago #7550
by Imamul
Contact Analysis was created by Imamul
Hi all,
I have simulated CG lipid monolayer and CG gold nanoparticle (AuNP). I did some analysis like order parameter of lipid, density profile along z-axis, area per lipid, lateral diffusion coefficient (just follow the tutorials). I want to calculate contact analysis other other analysis whatever you suggest. I have no idea how can I do contact analysis but saw some post use gmx mindist. In my simulation, the AuNP (3nm) interacts with lipids (1024) after 3 microsecond. Any advice for analysing the trajectories will be appreciated.
Regards
Imamul
I have simulated CG lipid monolayer and CG gold nanoparticle (AuNP). I did some analysis like order parameter of lipid, density profile along z-axis, area per lipid, lateral diffusion coefficient (just follow the tutorials). I want to calculate contact analysis other other analysis whatever you suggest. I have no idea how can I do contact analysis but saw some post use gmx mindist. In my simulation, the AuNP (3nm) interacts with lipids (1024) after 3 microsecond. Any advice for analysing the trajectories will be appreciated.
Regards
Imamul
Last edit: 6 years 1 month ago by Imamul.
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- riccardo
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6 years 1 month ago - 6 years 1 month ago #7551
by riccardo
Replied by riccardo on topic Contact Analysis
Hi Imamul,
Supposing you want to compute the no. of contacts between the lipids and the AuNP, you need something like this:
echo 0 1 | gmx mindist -n index.ndx -f traj.tc -on contacts_vs_time.xvg -d 0.6 -od mindist.xvg
where "index.ndx" is an index containing 2 groups: the first with all the lipid beads, the second with all the AuNP beads. "0.6" is the cutoff distance - we usually use 0.6. "contacts_vs_time.xvg" is what you want: the number of lipids-AuNP contacts at each trajectory frame.
Supposing you want to compute the no. of contacts between the lipids and the AuNP, you need something like this:
echo 0 1 | gmx mindist -n index.ndx -f traj.tc -on contacts_vs_time.xvg -d 0.6 -od mindist.xvg
where "index.ndx" is an index containing 2 groups: the first with all the lipid beads, the second with all the AuNP beads. "0.6" is the cutoff distance - we usually use 0.6. "contacts_vs_time.xvg" is what you want: the number of lipids-AuNP contacts at each trajectory frame.
Last edit: 6 years 1 month ago by riccardo.
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- Imamul
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6 years 1 month ago #7553
by Imamul
Replied by Imamul on topic Contact Analysis
Hi Riccardo,
Thank you for your quick reply. I am trying to follow your advice. Is there any other analysis that can I do?
Regards
Imamul
Thank you for your quick reply. I am trying to follow your advice. Is there any other analysis that can I do?
Regards
Imamul
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- riccardo
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6 years 1 month ago #7555
by riccardo
Replied by riccardo on topic Contact Analysis
Well, I would say that it depends on what you want to know about the system / what your research question is.
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- Imamul
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6 years 1 month ago #7557
by Imamul
Replied by Imamul on topic Contact Analysis
Hi Riccardo,
I did the contact analysis and it was the number of contact of two group vs time. But for my case, if I want to calculate the the number of contact of lipids vs number of contact of AuNP molecules, is it possible? I tried with different options of gmx mindist like "-or" option but it calculate the distance of AuNP vs number of lipid.
Thanks in advance.
Regards
Imamul
I did the contact analysis and it was the number of contact of two group vs time. But for my case, if I want to calculate the the number of contact of lipids vs number of contact of AuNP molecules, is it possible? I tried with different options of gmx mindist like "-or" option but it calculate the distance of AuNP vs number of lipid.
Thanks in advance.
Regards
Imamul
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- riccardo
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6 years 1 month ago #7558
by riccardo
Replied by riccardo on topic Contact Analysis
I'm not sure I fully understand.
If you want AuNP-lipid contacts over time, you used the command I wrote above, where you specify between which groups the contacts need be computed with the index file. In that case, your index.ndx should look like this:
[lipids_beads]
1 2 3 4 5 ..... N
[AuNP_beads]
N+1 N+2 ..... M
where N is the last lipid bead, N+1 the first AuNP bead, and M the last AuNP bead.
Or do you want to compute some other contacts? If so, between what?
If you want AuNP-lipid contacts over time, you used the command I wrote above, where you specify between which groups the contacts need be computed with the index file. In that case, your index.ndx should look like this:
[lipids_beads]
1 2 3 4 5 ..... N
[AuNP_beads]
N+1 N+2 ..... M
where N is the last lipid bead, N+1 the first AuNP bead, and M the last AuNP bead.
Or do you want to compute some other contacts? If so, between what?
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- Imamul
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6 years 1 month ago #7562
by Imamul
Replied by Imamul on topic Contact Analysis
Thank you Riccardo for your quick reply. I got the results of AuNP-lipid contacts over time by following your instruction.Actually in my previous post I wanted to calculate either the number of lipid_beads contact particularly to a single Au_beads or the number of Au_beads contact particularly ro a single lipid_beads. More specific, how many lipids or lipid_beads contact to a single Au_bead?
Thanks again.
Regards
Imamul
Thanks again.
Regards
Imamul
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- riccardo
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6 years 1 month ago #7563
by riccardo
Replied by riccardo on topic Contact Analysis
Alright, I see now. Well, if you want to compute the lipid contacts per Au bead, I would set up the following index (compare also to the previous one):
[lipids_beads]
1 2 3 4 5 ..... N
[AuNP_bead_1]
N+1
[AuNP_bead_2]
N+2
[AuNP_bead_...]
...
[AuNP_bead_...]
...
[AuNP_bead_M]
M
Then, by repeating the command above a number of times, you will get the no. of lipids contact each Au bead makes over time. The commands you need to run should look like this:
echo 0 1 | gmx mindist -n index.ndx -f traj.xtc -on contacts_vs_time_lipids-Au_bead_1.xvg -d 0.6 -od mindist.xvg
echo 0 2 | gmx mindist -n index.ndx -f traj.xtc -on contacts_vs_time_lipids-Au_bead_2.xvg -d 0.6 -od mindist.xvg
echo 0 3 | gmx mindist -n index.ndx -f traj.xtc -on contacts_vs_time_lipids-Au_bead_3.xvg -d 0.6 -od mindist.xvg
etc.
Hope this helps!
[lipids_beads]
1 2 3 4 5 ..... N
[AuNP_bead_1]
N+1
[AuNP_bead_2]
N+2
[AuNP_bead_...]
...
[AuNP_bead_...]
...
[AuNP_bead_M]
M
Then, by repeating the command above a number of times, you will get the no. of lipids contact each Au bead makes over time. The commands you need to run should look like this:
echo 0 1 | gmx mindist -n index.ndx -f traj.xtc -on contacts_vs_time_lipids-Au_bead_1.xvg -d 0.6 -od mindist.xvg
echo 0 2 | gmx mindist -n index.ndx -f traj.xtc -on contacts_vs_time_lipids-Au_bead_2.xvg -d 0.6 -od mindist.xvg
echo 0 3 | gmx mindist -n index.ndx -f traj.xtc -on contacts_vs_time_lipids-Au_bead_3.xvg -d 0.6 -od mindist.xvg
etc.
Hope this helps!
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- Imamul
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6 years 1 month ago #7565
by Imamul
Replied by Imamul on topic Contact Analysis
Thank You so much Riccardo ....
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