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normal Tilted Gel Phase Directionality

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12 years 8 months ago #772 by maxcw
Tilted Gel Phase Directionality was created by maxcw
I downloaded the files to simulate the tilted gel phase from the MARTINI website. I checked that the average angle between the lipid chains and the z axis is indeed about 30 degrees. But I found that there is no uniform tilt direction to the molecules-- they all point in random directions. So my simulation does not seem to look like the uniformly tilted picture in the Marrink, Risselada, and Mark 2005 paper (Fig. 14). I didn't change any of the files I download and I'm using GROMACS 4.0.2.

I would like to simulate the uniformly tilted gel phase, so can someone please tell me if I'm doing something wrong? Are the tilt parameters used in the 2005 paper different from what is on the website?

Thank you in advance!

Max

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12 years 8 months ago #774 by xavier
Replied by xavier on topic Tilted Gel Phase Directionality
The tilt should be pretty much oriented ... did you simulate enough?

maxcw wrote: I downloaded the files to simulate the tilted gel phase from the MARTINI website. I checked that the average angle between the lipid chains and the z axis is indeed about 30 degrees. But I found that there is no uniform tilt direction to the molecules-- they all point in random directions. So my simulation does not seem to look like the uniformly tilted picture in the Marrink, Risselada, and Mark 2005 paper (Fig. 14). I didn't change any of the files I download and I'm using GROMACS 4.0.2.

I would like to simulate the uniformly tilted gel phase, so can someone please tell me if I'm doing something wrong? Are the tilt parameters used in the 2005 paper different from what is on the website?

Thank you in advance!

Max

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12 years 8 months ago #786 by maxcw
Replied by maxcw on topic Tilted Gel Phase Directionality
I have run it for microseconds as a single patch as well as a 4x4 replicated patch. It has never become ordered. Another person in my group also ran the simulation independently and got the same thing. I can show you a snapshot if you'd like. Have you achieved a tilted gel phase using the files from this website?

Thanks,

Max

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12 years 8 months ago #787 by xavier
Replied by xavier on topic Tilted Gel Phase Directionality
No I have not tried to get the tilted gel phase. Did you use the modified itp file?

maxcw wrote: I have run it for microseconds as a single patch as well as a 4x4 replicated patch. It has never become ordered. Another person in my group also ran the simulation independently and got the same thing. I can show you a snapshot if you'd like. Have you achieved a tilted gel phase using the files from this website?

Thanks,

Max

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12 years 8 months ago #788 by maxcw
Replied by maxcw on topic Tilted Gel Phase Directionality
Yes I used

dppc_gel.gro
dppc_gel.mdp
dppc_gel.top
martini_v2.0_tilt.itp
martini_v2.0_lipids_tilt.itp

without changing any of the files.

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12 years 8 months ago #789 by xavier
Replied by xavier on topic Tilted Gel Phase Directionality
Could you check that you did everything correctly. This should be sorted out. I'll try myself to reproduce the results.

maxcw wrote: Yes I used

dppc_gel.gro
dppc_gel.mdp
dppc_gel.top
martini_v2.0_tilt.itp
martini_v2.0_lipids_tilt.itp

without changing any of the files.

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12 years 8 months ago #790 by maxcw
Replied by maxcw on topic Tilted Gel Phase Directionality
I have checked everything I know how to check. Thanks for trying it on your end!!

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12 years 7 months ago #791 by xavier
Replied by xavier on topic Tilted Gel Phase Directionality
Just to let you know that the files posted on the Martini webpage are not optimal to reproduce the tilted gel phase for DPPC. We are working on getting new files.

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