I want a big DMPC lipid system (>256 DMPC) for my protein to do MD using Gromacs 4.5.5. However I am not able to combine two DMPC molecules along with water as presented in Tieleman sites. Pleas kindly help me in designing a bigger system of DMPC with water for MD analysis.
Thanking You
Bikash
Osaka University, Japan
Dear Bikash,
Please describe the problem in more detail. At what stage is a problem?
How are you preparing your system? Is it a monolayer or bilayer? First have the energy minimized .pdb structure of a dmpc molecule. Then prepare monolayer or bilayer using the coordinates of the .pdb file. Then add water to the system.
Thanx all.. I have solved this problem. But I am very much thankful to you all (Dr. Alexey, Dr. Uttam and few otehr people). I prepared and minimized my big system for my work.
Thanking You All
Yours sincerely
Bikash
I know that you have solved your problem, and I congratulate you. But, by the way, an excellent software to construct systems is packmol: http://www.ime.unicamp.br/~martinez/packmol/
You can use an stabilized bilayer, and extend it or construct it from the begining (lipid by lipid).
Of course you need to check your models!!! It is a mathematical program and you are the brain, so if you do it wrong it is not the software problem. I mean, you need to check what you obtain, and perhaps you have overlaps, that you could solved stabilizing with a small dt, at first, then you could run your system without problem.
dear Bikash,
last week i performed a similar project with DPPC lipid.
For more information you can contact me via this email :
Ok, I agree. I experienced this problem once, when I constructed a monolayer. But if you check your system with VMD, and then you edit your .gro box size, you do not have any more problem.
By the way, I agree that your recomendation is a good tool too, but I consider that packmol is more general, it can be use for many more things than create lipid supra-structures.
FYI, you can use CHARMM GUI to give you the initial structure, and then apply whatever force field you want. i.e. it doesn't have to be CHARMM.
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