[gmx-users] Free energy calculations - desolvation energy of Na+

[Justin A. Lemkul]

eva.pluharova at marge.uochb.cas.cz wrote:
>  Hello all,
> 
>  I am trying calculate desolvation free energy of Na+ in water using option
>  couple-moltype, not by creating B-topology in the .top file.
> 
>  At first, I switched off coulombic interaction using:
> 
>  couple-moltype           = Na+
>  couple-lambda0           = vdw-q
>  couple-lambda1           = vdw
> 
>  Then I tried to switch off LJ interaction using couple-lambda0 = vdw and
>  couple-lambda1 = none, but obtained this warning:
> 
>  WARNING 1 [file equil_NVT000.mdp, line 95]:
>    For proper sampling of the (nearly) decoupled state, stochastic dynamics
>  should be used
> 
>  This is strange, because my .mdp file has only 94 lines.
> 

Regardless of the line number, the error message is pretty explicit - you 
probably have "integrator = md" in your .mdp file when you should have 
"integrator = sd."

-Justin

>  Thanks in advance for any help or suggestion.
> 
>  Best,
> 
>  Eva
> 
>  For convenience, I am pasting weak coupling algorithm section and free
>  energy section from my .mdp file. The simulation was performed at constant
>  volume using strong temperature coupling, since it was an equilibration
>  run.
> 
>  ; OPTIONS FOR WEAK COUPLING ALGORITHMS
>  Tcoupl                   = v-rescale
>  tc-grps                  = system
>  tau_t                    = 0.1
>  ref_t                    = 300
>  nsttcouple               = 1
> 
>  ; Free energy control stuff
>  free_energy              = yes
>  init_lambda              = 0.0
>  delta_lambda             = 0
>  foreign_lambda           = 0.1
>  sc-alpha                 = 0.7
>  sc-power                 = 1
>  sc-sigma                 = 0.3
>  nstdhdl                  = 10
>  separate-dhdl-file       = yes
>  dhdl-derivatives         = yes
>  dh_hist_size             = 0
>  dh_hist_spacing          = 0.1
>  couple-moltype           = Na+
>  couple-lambda0           = vdw
>  couple-lambda1           = none
>  couple-intramol          = no
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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