Re: [gmx-users] Mass in GMX topology

2013-07-13 Thread Dr. Vitaly Chaban
On Thu, Jul 11, 2013 at 1:17 PM, Steven Neumann wrote: > Thank you. Another question: Does RDF depends on the mass of the atom? On > the one hand it gives different value of the force in equation of motion > but on the other hand velocities are rescaled with a thermostat. > > It does not. Provide

Re: [gmx-users] Mass in GMX topology

2013-07-11 Thread Steven Neumann
I have the same feeling, thank you. But in general mass can influence the equilibrium property so I guess yes. Steven On Thu, Jul 11, 2013 at 1:27 PM, Justin Lemkul wrote: > > > On 7/11/13 8:17 AM, Steven Neumann wrote: > >> Thank you. Another question: Does RDF depends on the mass of the atom

Re: [gmx-users] Mass in GMX topology

2013-07-11 Thread Justin Lemkul
On 7/11/13 8:17 AM, Steven Neumann wrote: Thank you. Another question: Does RDF depends on the mass of the atom? On the one hand it gives different value of the force in equation of motion but on the other hand velocities are rescaled with a thermostat. My impression would be that the masses

Re: [gmx-users] Mass in GMX topology

2013-07-11 Thread Steven Neumann
Thank you. Another question: Does RDF depends on the mass of the atom? On the one hand it gives different value of the force in equation of motion but on the other hand velocities are rescaled with a thermostat. Steven On Thu, Jul 11, 2013 at 12:57 PM, Justin Lemkul wrote: > > > On 7/11/13 7:5

Re: [gmx-users] Mass in GMX topology

2013-07-11 Thread Justin Lemkul
On 7/11/13 7:54 AM, Steven Neumann wrote: Dear Users, Can you please write me where gromacs does read the mass of each atom: Is that the [atoms] under [moleculetype] or from [atomtypes] ? I wish to assign different mass for two different beads of the same type in my topology. It is taken fr

[gmx-users] Mass in GMX topology

2013-07-11 Thread Steven Neumann
Dear Users, Can you please write me where gromacs does read the mass of each atom: Is that the [atoms] under [moleculetype] or from [atomtypes] ? I wish to assign different mass for two different beads of the same type in my topology. Steven -- gmx-users mailing listgmx-users@gromacs.org htt