# Solvent deformation during NVT equilibration
**URL:** https://gromacs.bioexcel.eu/t/solvent-deformation-during-nvt-equilibration/8809
**Category:** User discussions
**Created:** [April 6, 2024, 11:08pm UTC](https://gromacs.bioexcel.eu/t/solvent-deformation-during-nvt-equilibration/8809 "2024-04-06T23:08:40Z")
**Posts on this page:** 2
**Page:** 1
### Author:  [@lachrymator](https://gromacs.bioexcel.eu/u/lachrymator)
#### Post date: [April 6, 2024, 11:08pm UTC](https://gromacs.bioexcel.eu/t/solvent-deformation-during-nvt-equilibration/8809/1 "2024-04-06T23:08:40Z")
GROMACS version:2023
GROMACS modification: No
Here post your question
Upon doing a standard NVT equilibration run, with the following parameters:
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 500000 ; 2 \* 500000 = 1000 ps
dt = 0.002 ; 2 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 ; 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 = PME ; 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 = Protein Non-Protein ; 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 = 310 ; temperature for Maxwell distribution
gen\_seed = -1 ; generate a random seed
The solvent box starts off as normal, then deforms after about 50 steps to:
What is happening here? Upon doing the NPT equilibration it seems to return to the proper size. The production run seems normal. Should I be concerned about this NVT step?
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### Author:  [@Seyilaxa](https://gromacs.bioexcel.eu/u/Seyilaxa)
#### Post date: [April 7, 2024, 4:18am UTC](https://gromacs.bioexcel.eu/t/solvent-deformation-during-nvt-equilibration/8809/2 "2024-04-07T04:18:15Z")
The size of box is constant in NVT step, so sometimes the atoms would aggregate due to the force. It means it is better to use thermostat to equilibrate the system when the vacuum space appears. If the NPT and production run normally, this would not be a serious issue.