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

[André Farias de Moura]

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 mechanics reasoning is the
momentum of the particle, p=mv, which clearly changes during your
alchemical transformation. Put in another way: the phase space of the
system is a 6N dimensional space of positions and momenta, and you have
just perturbed the momenta part.

And by the way: that is a typical case in which Monte Carlo methods would
fail to reproduce an MD result, since only the configurational phase space
is sampled in MC (masses effects would have to be added afterwards,
assuming that some analytical result could be computed)

I hope it helps

Andre

On Fri, Aug 11, 2017 at 6:36 AM, deepak bapat <dubapat at gmail.com> wrote:

> 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 2006.)
>
> step 1: increase mass of atom from 6.94100 to 35.45300.
>
> Step 2: change LJ parameters of LI to LJ of CL
>
>
> Now my doubt is in step 1:  i get non zero free energy values.
>
> *required nonbonded.itp file content is*
>
> ;LI+
> opls_406   LI  3   6.94100     0.000       A    2.8700e-01 2.0929e-03
> ; Li+ parameters from jensen and jorgensen JCTC 2006 2 1499-1509
>
> ;LI+ grown
> opls_407   LI  17   35.45300     0.000       A    2.8700e-01 2.0929e-03
> ; Li+ parameters from jensen and jorgensen JCTC 2006 2 1499-1509 ;; Mass of
> chlorine
>
>
> *LI.itp file content of alchemical transformation for mass is*
> [ atoms ]
> ; id    at type     res nr  residu name at name  cg nr  charge   mass
> 1       opls_406    1       LI          LI       1      0.0        6.941
> opls_407 0.0 35.45300
>
>
> *.mdp file used is as follows*
>
>
> integrator             = sd
> tinit                      = 0
> dt                         = 0.001
> nsteps                  = 1000000
> nstcomm              = 100
> nstxout                 = 0
> nstvout                 = 0
> nstfout                  = 0
> nstlog                   = 5000
> nstenergy             = 5000
> nstxtcout              = 500
> cutoff-scheme            = verlet
> nstlist                  = 10
> ns_type                  = grid
> pbc                      = xyz
> rlist                    = 1.0
> coulombtype              = PME
> rcoulomb                 = 1.0
> vdwtype                  = cutoff
> rvdw                     = 1.0
> DispCorr                  = EnerPres
> fourierspacing           = 0.12
> pme_order                = 6
> tc_grps                  = system
> tau_t                    = 1.0
> ref_t                    = 300
> Pcoupl                   = Parrinello-Rahman
> tau_p                    = 1.0
> compressibility          = 4.5e-05
> ref_p                    = 1.0
> free_energy              = yes
> init_lambda  = 0.05 ;;; depending on state, lambda value to be changed from
> 0 to 1 ;;;;;
> delta_lambda             = 0
> nstdhdl                  = 10
> gen_vel                  = no
> constraints              = h-bonds
> constraint-algorithm     = lincs
> continuation             = yes
> lincs-order              = 12
>
>
> Free enegy of step 1: i.e. mass transfomation is around +6.2 kJ/mol.
>
> In Gromacs 5.1.2 manual section 4.5 p.no 99 dependance of free energy on
> lambda equation is given.
>
> Now my doubt is if I am using the NPT ensemble then the total kinetic
> energy of the system should be constant i.e. summation(p^2/2m) which is
> being controlled by the thermostat.
>
> But i am getting non zero value in this case? Is it normal to get something
> like this or i have blundered somewhere?
>
> Will be happy to share input files if it helps.
>
> Thanks and Regards
>
> --
> Deepak U. Bapat
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-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090