[gmx-users] amber parameters in gromacs

Dear gromacs-users, I've been simulating a box of liquid glycerol. The parameter's I have used were taken from an article, whose authors achieved good agreement between their simulation and experiments. These authors used an amber force field and the software ORAC. I used exactly the same

[gmx-users] Re: amber parameters in gromacs

Hi, I used the GROMOS FF but changed the parameters (sigma, epsilon, charges, 1-4 interaction, combination rule for LJ, bond length strength, dihedrals, angles) so that they are equal to the parameters used by the other authors with their AMBER FF. The equations uses to calculate the energy

[gmx-users] Problems with g_hbond

Dear users, I'm running a simulation which uses ethanol as solvent. When using g_hbond the programm is able to recognize the solute's donors and acceptors, however it does not recognize any acceptors or donors of ethanol. Here is a part of my topology: [ atoms ] ; nr type resnr

[gmx-users] results of tpi

Hi everybody, I'm doing calculations with results, that I receive from tpi insertions. As I don't get the results I am heading for, I starded to wonder weather I interpretate the values in the columns of the xvg file correct. Hear is the head of the xvg files and next to it my interpretation

[gmx-users] many charges within one atom

Hi everybody, I'm trying to run simulations with a charge distribution within one single atom. Is there a way to create a molecule, in which every atom has a charge distribution - more charge points at one atom. Is it possible to run a simulation in a polarizable electric continuum in stead

[gmx-users] RE:appropriate values fot tau_t and tau_p

Hi, thank you for your help, Berk. The propertie I am looking for is the partial molar volume which can be calculated with this equation and a test particle insertion: vi=V^2exp(-bU)/Vexp(-bU) - V To find out the right mdp parameters I made test runs with a pure box of argon as vapour, so I

[gmx-users] appropriate values fot tau_t and tau_p

Dear all, I'm trying to receive thermal properties of a LJ liquid by performing a NPT simulation. To ensure the simulation is in the canonic ensemble, I've chosen the Nose-Hoover thermostat and the Parrinello-Rahmann barostat. I performed several runs with different values for tau_t and tau_p.

[gmx-users] pdb2gmx does not recognize residues

Hello everybody, I'm trying to set up a box with methane. Therefore I wrote a small pdb file which looks like this: ATOM 1 CH4CH4 11.0 1.0 1.0 1.0 0.0 ATOM 2 CH4CH4 20.5 0.5 0.5 1.0 0.0 ATOM 3 CH4CH4 3