# Pressure decreasing after npt equilibration **URL:** \ **Category:** User discussions\ **Tags:** mdp-parameters\ **Created:** [August 12, 2025, 12:46pm UTC](https://gromacs.bioexcel.eu/t/pressure-decreasing-after-npt-equilibration/12524 "2025-08-12T12:46:12Z")\ **Posts on this page:** 3\ **Page:** 1
**Author:** ![sanket\_singare](https://avatars.discourse-cdn.com/v4/letter/s/96bed5/32.png) [@sanket\_singare](https://gromacs.bioexcel.eu/u/sanket_singare)\ **Post date:** [August 12, 2025, 12:46pm UTC](https://gromacs.bioexcel.eu/t/pressure-decreasing-after-npt-equilibration/12524/1 "2025-08-12T12:46:12Z")
GROMACS version: GROMACS modification: Yes/No Here post your question Hello i have one issue the density is of my system during npt is nearly 1000kg/m3 , but for md production in npt ensemble it is showing less then 1000kg/m3 i will share my npt.mdp as well as md production. mdp * * * ; VARIOUS PREPROCESSING OPTIONS title = NPT simulation (constant number, pressure and temperature) cpp = /usr/bin/cpp define = -DPOSRES ; RUN CONTROL PARAMETERS integrator = md dt = 0.002 nsteps = 1000000 ; OUTPUT CONTROL OPTIONS nstxout = 2500 nstvout = 2500 nstfout = 0 nstlog = 2500 nstenergy = 2500 nstxtcout = 2500 xtc\_precision = 1000 xtc-grps = System energygrps = system ; NEIGHBORSEARCHING PARAMETERS nstlist = 10 ns-type = Grid pbc = xyz rlist = 1.0 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = pme pme\_order = 4 fourierspacing = 0.16 rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 ewald\_rtol = 0.00001 ; Temperature coupling Tcoupl = v-rescale tc-grps = system tau\_t = 1.0 ref\_t = 300 ; Pressure coupling Pcoupl = Berendsen Pcoupltype = Isotropic tau\_p = 1.0 compressibility = 4.5e-5 ref\_p = 1.0 DispCorr = EnerPres refcoord\_scaling = com ; GENERATE VELOCITIES FOR STARTUP RUN gen\_vel = no ; Assign velocities to particles by taking them randomly from a Maxwell distribution gen\_temp = 300 ; Temperature to generate corresponding Maxwell distribution gen\_seed = 135962 ; Seed for (semi) random number generation. ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = lincs continuation = yes shake-tol = 0.0001 ; VARIOUS PREPROCESSING OPTIONS title = Production Simulation cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS integrator = md tinit = 0 ; Starting time dt = 0.002 ; 2 femtosecond time step for integration nsteps = 5000000 ; 10 ns ; OUTPUT CONTROL OPTIONS nstxout = 100000 ; Writing full precision coordinates d nstvout = 100000 ; Writing velocities d nstfout = 0 ; Not writing forces nstlog = 50000 ; Writing to the log file nstenergy = 1000 ; Writing out energy information nstxtcout = 1000 ; Writing coordinates xtc\_precision = 1000 xtc-grps = system energygrps = system ; NEIGHBORSEARCHING PARAMETERS nstlist = 10 ns-type = Grid pbc = xyz rlist = 1.0 ; OPTIONS FOR ELECTROSTATICS AND VDW coulombtype = pme pme\_order = 4 fourierspacing = 0.16 rcoulomb = 1.0 vdw-type = cut-off rvdw = 1.0 ewald\_rtol = 0.00001 ; Temperature coupling Tcoupl = v-rescale tc-grps = system tau\_t = 1.0 ref\_t = 300 ; Pressure coupling Pcoupl = Parrinello-Rahman Pcoupltype = Isotropic tau\_p = 2.0 compressibility = 4.5e-5 ref\_p = 1.0 DispCorr = EnerPres refcoord\_scaling = com ; GENERATE VELOCITIES FOR STARTUP RUN gen\_vel = no gen\_temp = 300 gen\_seed = 314629 ; OPTIONS FOR BONDS constraints = all-bonds constraint-algorithm = lincs continuation = yes shake-tol = 0.0001 ; Input file ; cpp = /usr/bin/cpp define = -DFLEXIBLE constraints = none integrator = steep nsteps = 10000 ; nstxout = 2500 nstvout = 2500 nstfout = 0 nstlog = 2500 nstenergy = 2500 ; Energy minimizing stuff ; emtol = 10 emstep = 0.01 nstcomm = 1 ns\_type = grid rlist = 1.0 rcoulomb = 1.0 rvdw = 1.0 Tcoupl = no Pcoupl = no gen\_vel = no pbc = xyz please resolve the problem ---
**Author:** ![michael.brunsteiner](https://avatars.discourse-cdn.com/v4/letter/m/7cd45c/32.png) [@michael.brunsteiner](https://gromacs.bioexcel.eu/u/michael.brunsteiner)\ **Post date:** [August 12, 2025, 7:25pm UTC](https://gromacs.bioexcel.eu/t/pressure-decreasing-after-npt-equilibration/12524/2 "2025-08-12T19:25:22Z")
the pressure in NVT is VERY sensitive to the precise volume. Thus, if you start an NVT simulation with the final structure of an equilibrated NPT run, you can easily end up with pressures far from the one used in the NPT simulation, 100 bar up or down is not uncommon. In most cases, if your pressure is off by a few tens of bars, you can ignore that. If you still want to make sure to get close to the desired pressure you can modify the box dimensions in the input structure file for the NVT to have exactly the average values from the NPT run, then do another short minimization+equilibration in NVT before starting production (this only works if the differences between the box dimensions of the final NPT structure and these averages are small (\< 1 A), in this case you also want to make sure to use a structure that has no molecules broken across periodic boundaries), but i repeat, usually you do not need to bother…. ---
**Author:** ![sanket\_singare](https://avatars.discourse-cdn.com/v4/letter/s/96bed5/32.png) [@sanket\_singare](https://gromacs.bioexcel.eu/u/sanket_singare)\ **Post date:** [August 14, 2025, 5:26am UTC](https://gromacs.bioexcel.eu/t/pressure-decreasing-after-npt-equilibration/12524/3 "2025-08-14T05:26:50Z")
Thanks for your reply can you please check my mdp file and verify if any correction needed? and please give the solution for the same.