[gmx-users] free energy and soft core

[Frauke Meyer]

Hi Stefano,

if electrostatics are zero, does this mean you do not have any charges
on your molecule atoms? Neither LJ interactions that are no first or
second neighbors (and thus not excluded)? Then you do not change
anything at all?

Otherwise if charges!=0 are turned off, bond lengths/angles will change
leading to a free energy difference.

Frauke

On Tue, 2004-08-10 at 13:27, Stefano Piana wrote:
> Hi,
> I am very much interested in this discussion about free energy 
> calculations as I am doing some myself. As this can be a related issue I 
> attach this mail to this topic.
> I am "vaporizing" a molecule from a solution by turning the LJ 
> parameters and the charges to 0 during a perturbation run.
> The funny thing is that if I vaporize the molecule alone (without water) 
> in a non-periodic system I still get a free energy difference although 
> there is no Coulomb or LJ interaction at all in the molecule (they are 
> exactly 0 in the .edr file) and no contribution to the kinetic energy as 
> I am not changing the masses.
> Energy                      Average       RMSD     Fluct.      Drift 
> Tot-Drift
> -------------------------------------------------------------------------------
> Angle                       10.4334    5.38315    4.38697   0.108069 
> 10.8071
> Proper Dih.                 4.84332     3.0113    3.00803 -0.00485981 
> -0.485991
> Improper Dih.             0.0462622  0.0583175  0.0582569 9.20078e-05 
> 0.00920096
> LJ (SR)                           0          0          0          0 
>        0
> Coulomb (SR)                      0          0          0          0 
>        0
> Potential                    15.323    5.86594    5.05137   0.103301 
> 10.3303
> Kinetic En.                 14.2877    5.47298    5.46365  0.0110618 
>   1.1062
> Total Energy                29.6107    4.23443    2.65159   0.114363 
> 11.4365
> Temperature                 312.437    119.681    119.477   0.241895 
>    24.19
> Pressure (bar)                    0          0          0          0 
>        0
> dVpot/dlambda              0.141056    4.96762    4.94791  0.0153115 
> 1.53118
> dEkin/dlambda                     0          0          0          0 
>        0
> Heat Capacity Cv:      15.9914 J/mol K (factor = 0.146731)
> ----------------------------------------------------------------------
> 
> The free energy difference that I obtain is small (0.141 kj mol-1) but 
> reproducible to the third decimal digit in runs of different length and 
> with different values for sc-alpha.
> Any idea of where this contribution is coming from?
> 
> Stefano
> 
> 
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