Re: [gmx-users] non zero free energy values in mass transformation

Hi Dan Thanks a lot. I haven't tried a simulation in vacuum yet. I'll give it a try. Deepak On Mon, Aug 14, 2017 at 9:05 PM, Dan Gil wrote: > Hi Deepak, > > I'd like to share a reference with you. http://www.tandfonline. > com/doi/abs/10.1080/00268970600893060 > > If

Re: [gmx-users] non zero free energy values in mass transformation

Hi Deepak, I'd like to share a reference with you. http://www.tandfonline. com/doi/abs/10.1080/00268970600893060 If you could take a look at results (14) versus (15), and results (28) versus (29)... You see that when only the potential energy is considered, the mass doesn't contribute to the

Re: [gmx-users] non zero free energy values in mass transformation

Hi To study the efect of particle mass on excess chemical potential i did test particle insertion (tpi) in SPC/E water. I created a lennard jones particle with very small LJ parameters so that the probability of gettining it inside the cavity increases. In one case I kept mass of tpi particle

Re: [gmx-users] non zero free energy values in mass transformation

Thank you Andre and Dan. I'll read more about. Deepak On Fri, Aug 11, 2017 at 7:35 PM, Dan Gil wrote: > Hi Deepak, > > I am battling the same problem too. I am doing free energy calculation for > heptane -> perfluoro-heptane in water. Also SPC/E water, Gromacs 5.1. > >

Re: [gmx-users] non zero free energy values in mass transformation

Hi Deepak, I am battling the same problem too. I am doing free energy calculation for heptane -> perfluoro-heptane in water. Also SPC/E water, Gromacs 5.1. Like Andre said, there is expected to be a free energy change when you change the mass of a particle. But if you do the same transformation

Re: [gmx-users] non zero free energy values in mass transformation

Deepak, I never did a mass perturbation myself, but I would expect some free energy change, since the translational partition function depends on the mass of the molecules. Also, having the same kinetic energy is not meaningful at all, the correct quantity you should always use in statistical

[gmx-users] non zero free energy values in mass transformation

Dear Gmx Users I am trying to find out free energy of transforming one neutral LI to one CL in aqueous solution. Water model is SPC/E. Gromacs version: 5.1.2 I am doing something like this Insert 1 Li olecule in water. (Li parameters were taken from Kasper P. Jensen and William L. Jorgensen