[gmx-users] Fwd: Gas phase simulation

[gozde ergin]

---------- Forwarded message ----------
From: gozde ergin <gozdeeergin at gmail.com>
Date: Wed, Apr 22, 2015 at 12:21 PM
Subject: Gas phase simulation
To: gromacs.org_gmx-users at maillist.sys.kth.se


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.
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 parameters
integrator     = md
dt                 = 0.002
nsteps          = 1000000   ; 2 ns
nstcomm     = 10
; Output parameters
nstxout        = 50000      ; every 100 ps
nstvout        = 50000
nstfout         = 5000
nstxtcout      = 5000
nstenergy     = 5000
; Bond parameters
constraint_algorithm       = lincs
constraints                      = all-bonds
continuation                   = yes
; Single-range cutoff scheme
nstlist               = 5
ns_type            = grid
rlist                  = 1.1
rcoulomb         = 1.1
rvdw                 = 1.1
; PME electrostatics parameters
coulombtype     = PME
fourierspacing   = 0.12
fourier_nx         = 0
fourier_ny         = 0
fourier_nz         = 0
pme_order        = 4
ewald_rtol        = 1e-5
optimize_fft      = yes
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tcoupl                   = nose-hoover
tc-grps                  = System
tau_t                    = 1.0
ref_t                    = 300
; Pressure coupling is off for NVT
Pcoupl                 = No
; Generate velocities is on
;gen_vel               = no
; Periodic boundary conditions are on in all directions
pbc                    = xyz
; Long-range dispersion correction
DispCorr            = EnerPres
; Pull code
pull                    = umbrella
pull_geometry   = distance
pull_dim            = N N Y
pull_start           = yes
pull_ngroups    = 1
pull_group0      = B
pull_group1      = A
pull_init1          = 0
pull_rate1          = 0.0
pull_k1             = 1000      ; kJ mol^-1 nm^-2
pull_nstxout    = 1000      ; every 1 ps
pull_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