Re: [gmx-users] mass changes in free energy calculations

Yes, usually it would be a waste of time and energy to change the mass. On Fri, Jun 20, 2008 at 10:17 PM, Qiang Li <[EMAIL PROTECTED]> wrote: > Thanks for clearing the doubt. > > Is that more easier to get equlibrium to use unchanged mass when doing LJ > turning on/off? > I ask this since I found

Re: [gmx-users] mass changes in free energy calculations

Thanks for clearing the doubt. Is that more easier to get equlibrium to use unchanged mass when doing LJ turning on/off? I ask this since I found the forwards and backwards mutation free energy are more consistant if I do not change the mass. Accidentally? LQ On Thu, Jun 19, 2008 at 4:26 AM, Dav

Re: [gmx-users] mass changes in free energy calculations

You can change the mass if you like. Basically, the net free energy change associated with changing the mass should end up being zero so it will be irrelevant. The mass of course affects the dynamics and things like the velocities, but based on equipartition you can convince yourself that the free

[gmx-users] mass changes in free energy calculations

Dear all, I am calculating FE using TI. I have a question about mutating existing atoms with different mass. for example, using ffG53a6 force field, in one case i need to mutate CH2 to CH3, should I use [ atoms ] 17CH3 2ALA CB 6 0 15.035 CH20