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soft network problem
- wzhwei173
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8 years 7 months ago #4849
by wzhwei173
soft network problem was created by wzhwei173
Hi,
I generate a 25 base pair A-helix type double strand DNA with soft elastic network and put it into polarizable water box and equilibrate with the martini_v2.1P-dna.itp. However, it seems that the DNA cannot maintain its structure very well (Please see attached picture of initial structure and the equilibrated structure). I use time step of 10fs and I have checked the top file that the RUBBER_BANDS is set correctly before the itp file. Is there any idea on where the problem may come from and how to solve it? Thanks!
[img size=160K] www.dropbox.com/s/ko6pqskjlbtgpp6/compare2.png?dl=0 [/img]
Best,
Wei
I generate a 25 base pair A-helix type double strand DNA with soft elastic network and put it into polarizable water box and equilibrate with the martini_v2.1P-dna.itp. However, it seems that the DNA cannot maintain its structure very well (Please see attached picture of initial structure and the equilibrated structure). I use time step of 10fs and I have checked the top file that the RUBBER_BANDS is set correctly before the itp file. Is there any idea on where the problem may come from and how to solve it? Thanks!
[img size=160K] www.dropbox.com/s/ko6pqskjlbtgpp6/compare2.png?dl=0 [/img]
Best,
Wei
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- jaakko
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8 years 7 months ago #4851
by jaakko
Replied by jaakko on topic soft network problem
Hi Wei,
have you ran it with stiff network without issues? Just as a check that the CGing part is ok.
The soft network can be "too soft" for A-helices, I'd recommend you to increase the force constant of the rubber bands in the itp file and seeing if that fixes the issue.
- Jaakko
have you ran it with stiff network without issues? Just as a check that the CGing part is ok.
The soft network can be "too soft" for A-helices, I'd recommend you to increase the force constant of the rubber bands in the itp file and seeing if that fixes the issue.
- Jaakko
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- wzhwei173
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8 years 7 months ago #4857
by wzhwei173
Replied by wzhwei173 on topic soft network problem
Hi Jakko,
Thank you very much for your reply! Yes, I have run with the stiff network and this simulation goes well.
I increased the force constant from 13 to 30, 50, 100 and 150. The shape of DNA including the stiff network case are shown here:
This image is hidden for guests.
It seems that only at force constant 150 and stiff network case, the shape of A-DNA looks acceptable. I also plot the Rg of DNA as a function of frame after a few ns of equilibrium:
This image is hidden for guests.
At force constant 150, the A-DNA seems to be stretched a little bit compared with the stiff network case.
Do you have any suggestion on whether to choose stiff network or soft network with large force constant to perform a realistic simulation of A-DNA? Thank you very much!
Best,
Wei
Thank you very much for your reply! Yes, I have run with the stiff network and this simulation goes well.
I increased the force constant from 13 to 30, 50, 100 and 150. The shape of DNA including the stiff network case are shown here:
This image is hidden for guests.
Please log in or register to see it.
It seems that only at force constant 150 and stiff network case, the shape of A-DNA looks acceptable. I also plot the Rg of DNA as a function of frame after a few ns of equilibrium:
This image is hidden for guests.
Please log in or register to see it.
At force constant 150, the A-DNA seems to be stretched a little bit compared with the stiff network case.
Do you have any suggestion on whether to choose stiff network or soft network with large force constant to perform a realistic simulation of A-DNA? Thank you very much!
Best,
Wei
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- jaakko
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8 years 7 months ago #4872
by jaakko
Replied by jaakko on topic soft network problem
Hi Wei,
unless you have specific reason for not using the stiff network I'd start with that. Then if you need more flexibility I'd recommend you to modify the network (cutoff, strength and which beads are part of it, I'll try to add a section about this to the DNA tutorial soon). First thing to try then would be using a stiff network with a slightly weaker force constant.
- Jaakko
unless you have specific reason for not using the stiff network I'd start with that. Then if you need more flexibility I'd recommend you to modify the network (cutoff, strength and which beads are part of it, I'll try to add a section about this to the DNA tutorial soon). First thing to try then would be using a stiff network with a slightly weaker force constant.
- Jaakko
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