[gmx-users] Bug in g_energy for calculating heat capacity?

Hi, all, Actually I think others have also noticed this "bug": g_energy often generate incorrect heat capacity. When I checked the source code of gmx_energy.c, I found the calculation of heat capacity is only related with the fluctuation of temperature, which is actually the algorithm for NVE

Re: [gmx-users] [Fwd: question about the torsional potential]

Dear David Thank you very much for your answer, but I'm interested to know what formula has been used in the case of the torsional potential: 1) V(fi) = k*(1+cos(n*fi-fi0)) or 2) V(fi) = k(1+cos(delta)*cos(n*fi)) If you do not knows this detail of the program. Could yo say me someone who

Re: [gmx-users] [Fwd: question about the torsional potential]

David van der Spoel wrote: I'm very new in the world of gromacs, but I have experience in simulation (Molecular Dynamics, Monte Carlo, Langevin Dynamics, etc) always using my own programs. Now I am starting a research in polyaniline (PANI) using GROMACS with a model potential that has been dedu

[gmx-users] [Fwd: question about the torsional potential]

I'm very new in the world of gromacs, but I have experience in simulation (Molecular Dynamics, Monte Carlo, Langevin Dynamics, etc) always using my own programs. Now I am starting a research in polyaniline (PANI) using GROMACS with a model potential that has been deduced from fisrt principles by

Re: [gmx-users] dihedral potential

Dear friends and Mark Thank you very much for your answer. I mean polyaniline (PANI). Obviously I have not mentioned the other parameters of the potential (stretching, bending, non bonded interaccions, etc), because I know how to modify the itp files in order to include the values of my m

Re: [gmx-users] problem in analyzing

hazizian wrote: Hi I want to analyze md. This md took 10 ns(1 ps) for a protein with 206 residue and 2 Mn plus about 17000 molecule solvent as water. then I construct extra group containig Protein+2 Mn with make_ndx comand. I did g_rmsf for extracting the average structure of the new grou

[gmx-users] problem in analyzing

Hi I want to analyze md. This md took 10 ns(1 ps) for a protein with 206 residue and 2 Mn plus about 17000 molecule solvent as water. then I construct extra group containig Protein+2 Mn with make_ndx comand. I did g_rmsf for extracting the average structure of the new group rmsd equilibrated