[gmx-users] Gas phase simulation

[gozde ergin]

Dear Gromacs users,

In order to estimate the free energy profile of water on organic
coated-water system I am using Gromacs umbrella option.
I put my water molecule far away from the bulk organic+water system and
pulled this molecule through the bulk.
When I checked the PMF profile I realized that gas phase PMF does not seems
correct.
Water molecule's PMF value in gas phase and in organic layer is same which
should not be. I also attached the the PMF figure.
Gas phase PMF should be smaller than organic layer.
I am using the same .mdp parameters for bulk and gas phase.
Maybe I need to change some parameters while simulating the gas phase.


Any help will be appreciated.

Here is my .mdp parameters:


























































*; Run parametersintegrator     = mddt                 =
0.002nsteps          = 1000000   ; 2 nsnstcomm     = 10; Output
parametersnstxout        = 50000      ; every 100 psnstvout        = 50000
nstfout         = 5000nstxtcout      = 5000nstenergy     = 5000; Bond
parametersconstraint_algorithm       = lincsconstraints
  = all-bondscontinuation                   = yes; Single-range cutoff
schemenstlist               = 5ns_type            = grid
rlist                  = 1.1rcoulomb         = 1.1rvdw                 =
1.1; PME electrostatics parameterscoulombtype     = PMEfourierspacing   =
0.12fourier_nx         = 0fourier_ny         = 0fourier_nz         =
0pme_order        = 4ewald_rtol        = 1e-5optimize_fft      = yes;
Temperature coupling; tcoupl is implicitly handled by the sd
integratortcoupl                   = nose-hoovertc-grps                  =
Systemtau_t                    = 1.0ref_t                    = 300;
Pressure coupling is off for NVTPcoupl                 = No; Generate
velocities is on ;gen_vel               = no ; Periodic boundary conditions
are on in all directionspbc                    = xyz; Long-range dispersion
correctionDispCorr            = EnerPres; Pull codepull
= umbrellapull_geometry   = distancepull_dim            = N N
Ypull_start           = yes pull_ngroups    = 1pull_group0      =
Bpull_group1      = Apull_init1          = 0pull_rate1          =
0.0pull_k1             = 1000      ; kJ mol^-1 nm^-2pull_nstxout    =
1000      ; every 1 pspull_nstfout    = 1000      ; every 1 ps*

Best regards
-- 


Gözde Ergin
PhD student
Institut d'Ingénierie de l'Environnement (IIE)
Laboratoire de recherche sur les particules atmosphériques (APRL)
Ecole Polytechnique Fédérale de Lausanne (EPFL)
Station 2
1015 LAUSANNE / Suisse
office: GRC1517