[gmx-users] hydrophobicity

Hello Users I have a question about defining an atom to be either hydrophobic or hydrophilic. The gromacs manual shows that the maximum charge of the hydrophobic atom is 0.2. Does anyone know where this number is coming from? Any good reasons or references? Thank you in advance Sunjoo ___

[gmx-users] Re: gmx-users Digest, Vol 55, Issue 106

digest..." > > > Today's Topics: > > 1. Re: RE: [gmx-users] sedoheptulose (Bernhard Knapp) > 2. Re: sedoheptulose (Mark Abraham) > 3. large charge group (Sunjoo Lee) > 4. RE: large charge group (Berk Hess) > > > ---

[gmx-users] large charge group

Hello All Recently I have figured out the biggest problem that made my system unstable. I have parameterized a molecule pretty similar to octane. A single charge group used to be assigned to this molecule. With 1 nm cut-off distance for LJ interaction and the direct space for electrostatic interac

[gmx-users] charge density

Hello All We have tried to calculate the slab averaged charge density by adding up all the partial charges and dividing the sum by the slab volume. The charge density profile along the z axis for a single snapshot of a trajectory with our method was compared with the profile obtained from the g_po

[gmx-users] charge density

Hello All We have been trying to get the charge densities from the trajectory by using our in-house matlab code, which basically the same as a part of gmx_potential.c . z = x0[index[n][i]][axis]; if (z < 0) z += box[axis][axis]; if (z > box[axis][axi