[gmx-users] A Force Field Paper including Heme Proteins

Dear gromacs users, We just published a paper titled "Force field development for cofactors in the photosystem II" in Journal of Computational Chemistry, which includes the Amber03 compatible force field for heme-B and works well with heme proteins. You may use it for reference at your convenienc

[gmx-users] proper dihedral types in the topology

Dear man or madam, I have a question about the dihedral types in the topology. If I made the topology by hand, is it possible to combine the type 9 and type 3 for proper dihedrals? Any comment about that? Thanks. Best, Lu -- gmx-users mailing listgmx-users@gromacs.org http://lists.g

Re: [gmx-users] how to simulate crystals in Gromacs

late crystals in Gromacs From:"Mark Abraham" Date:Thu, April 7, 2011 12:05 pm To: "Discussion list for GROMACS users" ------ On 7/04/2011 1:55 PM, ZHANG Lu wrote: > Dear all, >I am

[gmx-users] how to simulate crystals in Gromacs

Dear all, I am now trying to simulate crystals in Gromacs. What I did was to convert the original crystal structure in cif format to pdb format and then use genconf to replicate the cells and run MD. Is it proper to do it in this way? Because the structure I got after MD run was completely

[gmx-users] spectral density calculation with GROMACS

Dear all, I am now developing a set of force field parameters and I want to calculate the spectral density with the normal mode analysis in GROMACS to check my parameters. The point here is that I want to get a plot (spectral density VS frequencies). Could anybody give me some slides or tutor