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

[eva.pluharova at marge.uochb.cas.cz]

Hi Justin,

thanks for this link:
http://lists.gromacs.org/pipermail/gmx-users/2003-June/006054.html
It clearly says, why sampling by MD is not proper.

Best,

Eva

>>  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
>>
>
> --
> ========================================
>
> 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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