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

[deepak bapat]

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 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 free energy. However this is based on
> the assumption that the mass between the two states are equal. The mass
> between Li+ and Cl- are rather different.
>
> Please correct me if I am wrong, but I believe TPI compares between two
> states, a solute in the ideal gas phase and the same solute in water (in
> your case). E.g. [Li]_idealGas -> [Li]_aqueous. The mass is not changing
> here.
>
> On the other hand TI considers two states with different species. In your
> case, it is [Li]_aqueous -> [Cl]_aqueous. The two states being compared is
> different than TPI. In TI, the masses of the solutes are different. I think
> the idea is that when you do a TI in water and do a TI in gas, the mass
> contributions to the free energy cancel out. Can you also try doing
> [Li]_idealGas -> [Cl]_idealGas? Hopefully, the free energy change due to
> the mass perturbation for the two transformations cancel out to zero.
>
> A disclaimer though, I am also working on a very similar problem without
> success (yet). I am very curious to see if this works out for you.
>
> Dan
>
>
> On Sun, Aug 13, 2017 at 11:08 PM, deepak bapat  wrote:
>
> > 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 equal to that of Lithium. In
> second
> > simulation the mass was equal to that of Chlorine atome.
> >
> > LJ parameters for tpi particles in both cases were 2.0e-02  7.64793e-02.
> >
> > In both cases the excess chemical potential was in the range of 0.0798
> > kJ/mol.
> >
> > tpi only considers energy as a function of coordinates only so i assume
> > that it would depend only on LJ parameters as long as we are delaing with
> > neutral systems.
> >
> > So looking at this I again come back to the mass perturbation which
> started
> > all this.
> >
> > Since I was doing NPT calculations at 300 K I expected that average total
> > kinetic energy of the system should not be different. The themostat would
> > just adjust velocity distribution so that it brings the temperature of
> the
> > system to the set temperature. Any increase or decrease in mass should be
> > accounted for by the thermostat.
> >
> > As I said, in free energy calculations I got non zero value. (~ +6.2
> > kJ/mol). So I am still worried about this non zero behavior.
> >
> > Thanks and regards
> >
> > Deepak
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > On Sat, Aug 12, 2017 at 10:11 AM, deepak bapat 
> wrote:
> >
> > > 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.
> > >>
> > >> 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
> > from
> > >> Li+ to Cl- in the gas phase, hopefully the free energy change will be
> > >> opposite and (approximately) equal. Have you tried doing this second
> > >> calculation [Li+ -> Cl-] in the gas phase? I think this website:
> > >> http://www.alchemistry.org/wiki/Thermodynamic_Cycle explains why this
> > >> second step might be needed better.
> > >>
> > >> Dan
> > >>
> > >> On Fri, Aug 11, 2017 at 9:37 AM, André Farias de Moura <
> mo...@ufscar.br
> > >
> > >> wrote:
> > >>
> > >> > 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
> > >> 

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

[Dan Gil]

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 free energy. However this is based on
the assumption that the mass between the two states are equal. The mass
between Li+ and Cl- are rather different.

Please correct me if I am wrong, but I believe TPI compares between two
states, a solute in the ideal gas phase and the same solute in water (in
your case). E.g. [Li]_idealGas -> [Li]_aqueous. The mass is not changing
here.

On the other hand TI considers two states with different species. In your
case, it is [Li]_aqueous -> [Cl]_aqueous. The two states being compared is
different than TPI. In TI, the masses of the solutes are different. I think
the idea is that when you do a TI in water and do a TI in gas, the mass
contributions to the free energy cancel out. Can you also try doing
[Li]_idealGas -> [Cl]_idealGas? Hopefully, the free energy change due to
the mass perturbation for the two transformations cancel out to zero.

A disclaimer though, I am also working on a very similar problem without
success (yet). I am very curious to see if this works out for you.

Dan


On Sun, Aug 13, 2017 at 11:08 PM, deepak bapat  wrote:

> 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 equal to that of Lithium. In second
> simulation the mass was equal to that of Chlorine atome.
>
> LJ parameters for tpi particles in both cases were 2.0e-02  7.64793e-02.
>
> In both cases the excess chemical potential was in the range of 0.0798
> kJ/mol.
>
> tpi only considers energy as a function of coordinates only so i assume
> that it would depend only on LJ parameters as long as we are delaing with
> neutral systems.
>
> So looking at this I again come back to the mass perturbation which started
> all this.
>
> Since I was doing NPT calculations at 300 K I expected that average total
> kinetic energy of the system should not be different. The themostat would
> just adjust velocity distribution so that it brings the temperature of the
> system to the set temperature. Any increase or decrease in mass should be
> accounted for by the thermostat.
>
> As I said, in free energy calculations I got non zero value. (~ +6.2
> kJ/mol). So I am still worried about this non zero behavior.
>
> Thanks and regards
>
> Deepak
>
>
>
>
>
>
>
>
>
>
>
> On Sat, Aug 12, 2017 at 10:11 AM, deepak bapat  wrote:
>
> > 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.
> >>
> >> 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
> from
> >> Li+ to Cl- in the gas phase, hopefully the free energy change will be
> >> opposite and (approximately) equal. Have you tried doing this second
> >> calculation [Li+ -> Cl-] in the gas phase? I think this website:
> >> http://www.alchemistry.org/wiki/Thermodynamic_Cycle explains why this
> >> second step might be needed better.
> >>
> >> Dan
> >>
> >> On Fri, Aug 11, 2017 at 9:37 AM, André Farias de Moura  >
> >> wrote:
> >>
> >> > 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 
> >> wrote:
> >> >
> >> > > Dear Gmx Users
> >> > >
> >> > > I am trying to find out 

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

[deepak bapat]

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 equal to that of Lithium. In second
simulation the mass was equal to that of Chlorine atome.

LJ parameters for tpi particles in both cases were 2.0e-02  7.64793e-02.

In both cases the excess chemical potential was in the range of 0.0798
kJ/mol.

tpi only considers energy as a function of coordinates only so i assume
that it would depend only on LJ parameters as long as we are delaing with
neutral systems.

So looking at this I again come back to the mass perturbation which started
all this.

Since I was doing NPT calculations at 300 K I expected that average total
kinetic energy of the system should not be different. The themostat would
just adjust velocity distribution so that it brings the temperature of the
system to the set temperature. Any increase or decrease in mass should be
accounted for by the thermostat.

As I said, in free energy calculations I got non zero value. (~ +6.2
kJ/mol). So I am still worried about this non zero behavior.

Thanks and regards

Deepak











On Sat, Aug 12, 2017 at 10:11 AM, deepak bapat  wrote:

> 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.
>>
>> 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 from
>> Li+ to Cl- in the gas phase, hopefully the free energy change will be
>> opposite and (approximately) equal. Have you tried doing this second
>> calculation [Li+ -> Cl-] in the gas phase? I think this website:
>> http://www.alchemistry.org/wiki/Thermodynamic_Cycle explains why this
>> second step might be needed better.
>>
>> Dan
>>
>> On Fri, Aug 11, 2017 at 9:37 AM, André Farias de Moura 
>> wrote:
>>
>> > 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 
>> 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   A2.8700e-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   A2.8700e-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 ]
>> > > ; idat type res nr  residu name at name  cg nr  charge   mass
>> > > 1   opls_4061   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  = 100
>> > > nstcomm  = 100
>> > > nstxout = 0
>> > > nstvout = 0
>> > > nstfout   

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

[deepak bapat]

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.
>
> 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 from
> Li+ to Cl- in the gas phase, hopefully the free energy change will be
> opposite and (approximately) equal. Have you tried doing this second
> calculation [Li+ -> Cl-] in the gas phase? I think this website:
> http://www.alchemistry.org/wiki/Thermodynamic_Cycle explains why this
> second step might be needed better.
>
> Dan
>
> On Fri, Aug 11, 2017 at 9:37 AM, André Farias de Moura 
> wrote:
>
> > 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  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   A2.8700e-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   A2.8700e-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 ]
> > > ; idat type res nr  residu name at name  cg nr  charge   mass
> > > 1   opls_4061   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  = 100
> > > 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 

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

[Dan Gil]

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 from
Li+ to Cl- in the gas phase, hopefully the free energy change will be
opposite and (approximately) equal. Have you tried doing this second
calculation [Li+ -> Cl-] in the gas phase? I think this website:
http://www.alchemistry.org/wiki/Thermodynamic_Cycle explains why this
second step might be needed better.

Dan

On Fri, Aug 11, 2017 at 9:37 AM, André Farias de Moura 
wrote:

> 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  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   A2.8700e-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   A2.8700e-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 ]
> > ; idat type res nr  residu name at name  cg nr  charge   mass
> > 1   opls_4061   LI  LI   1  0.06.941
> > opls_407 0.0 35.45300
> >
> >
> > *.mdp file used is as follows*
> >
> >
> > integrator = sd
> > tinit  = 0
> > dt = 0.001
> > nsteps  = 100
> > 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
> >
> > --
> > 

Re: [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  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   A2.8700e-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   A2.8700e-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 ]
> ; idat type res nr  residu name at name  cg nr  charge   mass
> 1   opls_4061   LI  LI   1  0.06.941
> opls_407 0.0 35.45300
>
>
> *.mdp file used is as follows*
>
>
> integrator = sd
> tinit  = 0
> dt = 0.001
> nsteps  = 100
> 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
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