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

eva.pluharova at marge.uochb.cas.cz eva.pluharova at marge.uochb.cas.cz
Mon Oct 25 11:58:18 CEST 2010

 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.

 Thanks in advance for any help or suggestion.



 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

 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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