[gmx-users] How to fix molecules in gromacs?

[Daniele Veclani]

Dear gromacs users.

I'm trying to fix a molecule inside the box. I want to use this molecule as
an immobile reference in the pulling simulations.

I can i do this? I have to use the position restraint or freezing Group?

I tried to use position restraint, but, by analyzing the trajectories,
I see that
the molecule out of the box.

This is my .top file:
-----------------------------------
; Topology of CNT and CFX
;-----------------------------------
#include "gromos54a7_atb.ff/forcefield.itp"

;-----------------------------------------------
; Uncomment the line with needed topology below
;-----------------------------------------------
; #include "zw"

#include "cipro.itp"

; #include cnt

#include "nano.itp"
#ifdef DPOSRES_0PCZ
#include "cnt-posre.itp"
#endif

#include "gromos54a7_atb.ff/spce.itp"

[ system ]
cnt-cipro
[ molecules ]
; Compound        nmols
AUT8             1
0PCZ             1
SOL              39030

This is may .mdp file:

;preprocessing
define                   = -DPOSRES_0PCZ
; Run control
integrator               = sd       ; Langevin dynamics
dt                       = 0.002
nsteps                   = 300000    ; 0.6 ns
nstcomm                  = 10
; Output control
nstxout                  = 5000
nstvout                  = 5000
nstfout                  = 5000
nstlog                   = 5000
nstenergy                = 5000
nstxout-compressed       = 5000
; Neighborsearching and short-range nonbonded interactions
cutoff-scheme            = verlet
nstlist                  = 10
ns_type                  = grid
pbc                      = xyz
rlist                    = 0.8
; Electrostatics
coulombtype              = PME
rcoulomb                 = 1.2
; van der Waals
vdwtype                  = cutoff
rvdw                     = 1.2
; Apply long range dispersion corrections for Energy and Pressure
DispCorr                  = EnerPres
; Spacing for the PME/PPPM FFT grid
fourierspacing           = 0.12
; EWALD/PME/PPPM parameters
pme_order                = 6
ewald_rtol               = 1e-06
epsilon_surface          = 0
; Temperature coupling
; tcoupl is implicitly handled by the sd integrator
tcoupl                   = Nose-Hoover
tc_grps                  = system
tau_t                    = 1.0
ref_t                    = 298.15
; Pressure coupling is on for pull
Pcoupl                   = Parrinello-Rahman
tau_p                    = 0.5
compressibility          = 4.5e-05
ref_p                    = 1.0
; Free energy control stuff
; Generate velocities to start
gen_vel                  = no
gen_temp                 = 298.15
gen_seed                 = -1
; options for bonds
constraints              = h-bonds  ; we only have C-H bonds here
; Type of constraint algorithm
constraint-algorithm     = lincs
; Do not constrain the starting configuration
continuation             = yes
; Highest order in the expansion of the constraint coupling matrix
lincs-order              = 4
lincs-iter               = 1
; Pull code
pull                    = umbrella
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = AUT8
pull_group2_name        = 0PCZ
pullgeometry            = distance      ; simple distance increase
pull_coord1_groups = 1 2
pull_dim                = N Y N
pull_coord1_rate        = 0.01          ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
pull_start              = yes

How can I fix this problem??

I use gromacs 5.0.4

Best regards
D.V.