Hello
I want to model interaction between C60 and few some chemical compounds in a box with water. Can anybody suggest me any software tool (except gromacs) for such kind of work ?
I would be very grateful for that.
Dear Vasyl
Good results for the interaction of compounds can be obtained using software NAMD code59 with CHARMM27 all-atom force field modified for your compounds (see.: Armen H. Poghosyan, Hrant H. Gharabekyan, Aram A. Shahinyan "Molecular Dynamics Simulation of DMPC / DPPC Mixed Bilayer ", International Journal of Modern Physics C Vol. 18, No. 1 (2007) 73-89; Armen H. Poghosyan, Levon H. Arsenyan, Hrant H. Gharabekyan, Joachim Koetz, Aram A. Shahinyan" Molecular Dynamics Study of Poly (diallyldimethylammonium chloride) (PDADMAC) / Sodium Dodecyl Sulfate (SDS) / Decanol / Water Systems " J. Phys. Chem. B 2009, 113, 1303-1310, Armen H. Poghosyan, Grigor A. Yeghiazaryan, Hrant H. Gharabekyan , Aram A. Shahinyan "The GROMACS and NAMD Software Packages Comparison" COMMUNICATIONS IN COMPUTATIONAL PHYSICS, Vol. 1 (2006), No. 4, pp. 736-743).
A.Shahinyan
You should be more specific - what exactly would be aim of your calculations? What do you want to reach?
Dear Vasyl
Good results for the interaction of compounds can be obtained using software NAMD code59 with CHARMM27 all-atom force field modified for your compounds (see.: Armen H. Poghosyan, Hrant H. Gharabekyan, Aram A. Shahinyan "Molecular Dynamics Simulation of DMPC / DPPC Mixed Bilayer ", International Journal of Modern Physics C Vol. 18, No. 1 (2007) 73-89; Armen H. Poghosyan, Levon H. Arsenyan, Hrant H. Gharabekyan, Joachim Koetz, Aram A. Shahinyan" Molecular Dynamics Study of Poly (diallyldimethylammonium chloride) (PDADMAC) / Sodium Dodecyl Sulfate (SDS) / Decanol / Water Systems " J. Phys. Chem. B 2009, 113, 1303-1310, Armen H. Poghosyan, Grigor A. Yeghiazaryan, Hrant H. Gharabekyan , Aram A. Shahinyan "The GROMACS and NAMD Software Packages Comparison" COMMUNICATIONS IN COMPUTATIONAL PHYSICS, Vol. 1 (2006), No. 4, pp. 736-743).
A.Shahinyan
I guess you are planning a few non-bonding aromatic (pi-) interactions with your compounds. I think you are to create a geometry in the cage of C60 with the compound looking for the most probable site of interaction of your compound and optimize the geometry using good a level of HF or DFT quantum chemical theory. Molecular electrostatic potential (MEP) profile of your compound should be a good starting point. Also you will have to calculate the energies of C60, and the compound individually at the same level of theory to determine the interaction energy. Best of luck.
A lot of answers so fast, thanks.
My friends are testing how mix of C60 and other compound effect on the few cancer cell lines. My task is to build а model how C60 and other compound could interact which each others in intracellular environment. As far as I understand, for such task I must:
- build the box with water and some concentration of cell ions (e. g. Na, K ...)
- add there my compounds. The distance between them must be in a range 0.5-1 nm.
- start simulation.
if U can correct something in above algorithm, please write it.
I'm able to do it in gromacs. But, I afraid that they ask a lot after gromacs, that is why I asked for some other software tool (easier).
I'll try to use NAMD then LAMMPS:) Thanks.
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