[gmx-users] Re: gmx-users Digest, Vol 78, Issue 186

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

Hi Justin,

thank you for suggestion about changing the integrator, but I would like
to know why it is not possible to sample properly by md under these
circumstances.

1. Do you know any papers about sampling efficiency of systems with almost
or completely switched off particles? How does it depend on the kind of
thermostat or barostat?

2. Note, that you can switch off the LJ particle also by creating B
topology with sigma and epsilon equal to 0 in the .top file, not using
couple-moltype. Doing so, there is no warning, but these approaches are
equivalent. This seems like internal inconsistency in Gromacs.

Thanks again for any hints.

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
>
> ========================================