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Insertion of cg-fullerens
- bbm
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10 months 4 weeks ago #9641
by bbm
Insertion of cg-fullerens was created by bbm
Dear Martini users,
I am a new user of martini forcefield in gromacs. I doing a c60-fullerene simulation in water using various concentrations of fullerene. I have downloaded the fullerene structure and parameters from the martini website and added different number of fullerene molecules in a simulation box using gmx insert-molecules and solvated the box with water molecules. However, during the insertion of fullerene I have not used the -radius 0.21 flag. I did not encounter any blowing up of the simulations, but in some cases the energy minimization step did not converge to Fmax < 10 (rather they stopped at 12 or 14 kJ mol-1 nm-1) and used up almost 14-15000 energy minimization steps and this is more prevalent for the more concentrated solutions. I would like to know is this okay or any kind of molecule if we insert (coarse-grained representation) we need to use -radius 0.21 to avoid addition of very closely spaced molecules? In case of ions how do we ensure this -radius 0.21 flag as genion tool in gromacs does not let us define the van der Waals radius? Any help/suggestions will be much appreciated.
I am a new user of martini forcefield in gromacs. I doing a c60-fullerene simulation in water using various concentrations of fullerene. I have downloaded the fullerene structure and parameters from the martini website and added different number of fullerene molecules in a simulation box using gmx insert-molecules and solvated the box with water molecules. However, during the insertion of fullerene I have not used the -radius 0.21 flag. I did not encounter any blowing up of the simulations, but in some cases the energy minimization step did not converge to Fmax < 10 (rather they stopped at 12 or 14 kJ mol-1 nm-1) and used up almost 14-15000 energy minimization steps and this is more prevalent for the more concentrated solutions. I would like to know is this okay or any kind of molecule if we insert (coarse-grained representation) we need to use -radius 0.21 to avoid addition of very closely spaced molecules? In case of ions how do we ensure this -radius 0.21 flag as genion tool in gromacs does not let us define the van der Waals radius? Any help/suggestions will be much appreciated.
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