Re: [gmx-users] force field parameters for Fe3O4?

Hello, I use AMBER force field. So, how about periodic structures? like inorganic nanosheet and nanotubes? Thank you so much On Fri, 13 Apr 2018, 14:50 Paul bauer, wrote: > Hello, > > this depends on the force field you are using. Some of them use > parameters from a

Re: [gmx-users] force field parameters for Fe3O4?

Hello, this depends on the force field you are using. Some of them use parameters from a QM optimization and partial charge calculation. But even then you need to be careful that the results from the QM are not just random numbers :) But I'm not sure myself how I would tackle something like

Re: [gmx-users] force field parameters for Fe3O4?

On Fri, 13 Apr 2018, 14:35 Paul bauer, wrote: > Hello, > > I would recommend that you check relevant publications for the > simulation of magnetite if people have tried to simulate it in solvent. > I could not find anything during a short search, but maybe you'll be >

Re: [gmx-users] force field parameters for Fe3O4?

Hello, I would recommend that you check relevant publications for the simulation of magnetite if people have tried to simulate it in solvent. I could not find anything during a short search, but maybe you'll be more successful. :) If there are no published parameters in the literature you will

[gmx-users] force field parameters for Fe3O4?

Dear gromacs users, I want to simulate a protein in different concentration of Fe3O4. How to obtain force field parameters of Fe3O4? Any help will highly be appreciated. Best, -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Polarizability analysis

Hi I did umbrella sampling and calculate PMF for different aminoacid in different distance from surface. Now i want to discuss about the results. First i used gmx sasa to prove that for example amino acid(tyrosine) with more surface (it's aromatic) had more binding energy in comparison to

[gmx-users] Gmx hbond

Hi, I have 2 questions, but please consider them 2 distinct questions and are not related. I did umbrella sapmling and calculate the PMF. Now i I want to calculate number of hydrogen bonds for amino acid in its initial distance(far from surface) and binding distance ( which is close to surface