[gmx-users] How to prevent velocity generation for my position restrained molecules ?

[Mohamed Abdelaal]

Hello everybody,

I am simulating the evaporation process for different atoms on a graphene
sheet and the z-coordinate of each graphene carbon atom was restrained
(using position restrain).

The energy minimization was successfully done without any errors

Then I started the equilibration, I have done the NVT. My nvt.mdp file
is written below. I have added the -DPOSRES to enable the position
restrain and I added temperature

 coupling for both the GRM (the graphene sheet molecules) and the G8LE
(The residue molecules; the molecules I am evaporating) then I wrote
generate velocity = yes.

After finishing the NVT  equilibration, I checked the nvt.gro file and
the problem now is that, I have velocity for both the graphene
molecules (which supposed to be position

restrained) and for the residue. How can I generate velocity for the
residue only (G8LE) and make sure that the graphene sheet is
restrained.


title                   =  NVT equilibration
define                  = -DPOSRES  ; position restrain the protein
; Run parameters
integrator              = md        ; leap-frog integrator
nsteps                  = 50000     ; 2 * 50000 = 100 ps
dt                      = 0.0005     ; 0.5 fs
; Output control
nstxout                 = 500       ; save coordinates every 1.0 ps
nstvout                 = 500       ; save velocities every 1.0 ps
nstenergy               = 500       ; save energies every 1.0 ps
nstlog                  = 500       ; update log file every 1.0 ps
; Bond parameters
continuation            = no        ; first dynamics run
constraint_algorithm    = lincs     ; holonomic constraints
constraints             = h-bonds ; bonds involving H are constrained
lincs_iter              = 1         ; accuracy of LINCS
lincs_order             = 4         ; also related to accuracy
; Nonbonded settings all-angles
cutoff-scheme           = Verlet    ; Buffered neighbor searching
ns_type                 = grid      ; search neighboring grid cells
nstlist                 = 10        ; 20 fs, largely irrelevant with Verlet
rcoulomb                = 1.0       ; short-range electrostatic cutoff (in nm)
rvdw                    = 1.0       ; short-range van der Waals cutoff (in nm)
DispCorr                = EnerPres  ; account for cut-off vdW scheme
; Electrostatics
coulombtype             = cut-off   ; Particle Mesh Ewald for
long-range electrostatics
pme_order               = 4         ; cubic interpolation
fourierspacing          = 0.16      ; grid spacing for FFT
; Temperature coupling is on
tcoupl                  = V-rescale             ; modified Berendsen thermostat
tc-grps                 = G8LE GRM  ; two coupling groups - more accurate
tau_t                   = 0.1   0.1  ; time constant, in ps
ref_t                   = 300   300 ; reference temperature, one for
each group, in K
; Pressure coupling is off
pcoupl                  = no        ; no pressure coupling in NVT
; Periodic boundary conditions
pbc                     = xyz       ; 3-D PBC
; Velocity generation
gen_vel                 = yes       ; assign velocities from Maxwell
distribution
gen_temp                = 300       ; temperature for Maxwell distribution
gen_seed                = -1        ; generate a random seed
periodic_molecules = yes


Many thanks,

Mohamed