# To Freeze Graphene sheet

**URL:** https://gromacs.bioexcel.eu/t/to-freeze-graphene-sheet/7387
**Category:** User discussions
**Tags:** mdp-parameters
**Created:** [October 14, 2023, 9:20am UTC](https://gromacs.bioexcel.eu/t/to-freeze-graphene-sheet/7387 "2023-10-14T09:20:45Z")
**Posts on this page:** 1
**Page:** 1

<div class="post-metadata">

### Author: ![Piyusa](https://avatars.discourse-cdn.com/v4/letter/p/46a35a/32.png) [@Piyusa](https://gromacs.bioexcel.eu/u/Piyusa)
#### Post date: [October 14, 2023, 9:20am UTC](https://gromacs.bioexcel.eu/t/to-freeze-graphene-sheet/7387/1 "2023-10-14T09:20:46Z")

</div>

GROMACS version:  
GROMACS modification: Yes/No  
Here post your question  
I am doing a simulation with a Graphene sheet with solvent. I want to make the graphene freeze in its initial position but after heating it is moving up. Below I have attached the mdp file and initial and after-heating snap. Can anyone please suggest what I need to impose to make the graphene sheet frozen in its position?

mdp file,  
title = Graphene-LiPF6-EC Heating  
;define = -DPOSRES ; position restrain the protein  
; Run parameters  
integrator = md ; Stochastic or velocity Langevin dynamics  
nsteps = 1000000 ; 1 \* 1000000 = 1000 ps  
dt = 0.001 ; 1 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  
cutoff-scheme = Verlet ; Buffered neighbor searching  
ns\_type = grid ; search neighboring grid cells  
nstlist = 10 ; 10 fs, largely irrelevant with Verlet  
rlist = 0.6  
vdwtype = cutoff  
vdw-modifier = Potential-switch  
rvdw-switch = 0.4  
rvdw = 0.6

; Electrostatics  
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics  
rcoulomb = 0.6 ; short-range electrostatic cutoff (in nm)  
pme\_order = 4 ; cubic interpolation  
fourierspacing = 0.16 ; grid spacing for FFT  
DispCorr = EnerPres ; account for cut-off vdW scheme

; Temperature coupling is on  
tcoupl = Nose-Hoover ; More accurate thermostat  
tc-grps = GRA RES2 RES3 RES4 ; two coupling groups - more accurate  
tau\_t = 0.2 0.2 0.2 0.2 ; time constant, in ps  
ref\_t = 298 298 298 298 ; 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 = 298 ; temperature for Maxwell distribution  
gen\_seed = -1 ; generate a random seed

;nstcomm = 100  
;comm\_mode = linear  
;comm\_grps = SYSTEM

; To freeze molecule  
 ![after-heating](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/8/880a40ffb0d3b4e4287a90a44015e3a9f260e739.jpeg)

freezegrps = GRA  
freezedim = Y Y Y  
 ![initial](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/c/c74bec4ecc80d751ede51c59ec92158e55805562.jpeg)

Thanks in Advance.