[gmx-users] kappa in Generalized reaction field

Hi all I'm going to ask about the definition of kappa in Generalized Reaction-field. In manual-3.3.pdf and manual-3.2.pdf (eq 4.17), kappa**2 = ...SUM (c_i * z_i) But, in Ref.51 (eq 5), kappa**2 = ...SUM (c_i * (z_i)**2) Is eq.4.17 correct? ___ g

[gmx-users] kappa in Generalized reaction field

> > > >Do we want to keep this code at all? > > Good question. > I think simulating ionic solutions with reaction-field causes large > artifacts, > unless the concentration is very high and the cut-off quite long. > PME is a much better choice. Really? Recently, I read a paper, which shows the G

[gmx-users] trjconv for hexa-meric protein

Hi I simulate a hexa-meric protein (443*6=2658 residues with about 9 water) Especially, I'm interested in water behavior around the protein. The 1ns simulation is finished normally, but trjconv produces abnormal structure. For example, the protein go outside my waterbox, water molecules are d

[gmx-users] pdb2gmx(ver3.3) contain bug?

-0.5814.0067 ; qtot 1 > 1521FE152 HEME FE6430.4 55.847 ; qtot 2.4 >... > [bonds] >... > 926 1521 2 The line '926 1521 2' does not exist in .top file made by GROMACS 3.3. For your information, there are n

[gmx-users] Re: pdb2gmx(ver3.3) contain bug?

> Tomoshi Kameda wrote: > > Hi > > > > > > I'm going to simulate a HEME-Protein complex using GROMACS 3.3, and try > > > > pdb2gmx -f pdb1a6n.ent > > > > and select > > 0: GROMOS96 43a1 force field > > > &g