pressure non converge with external pressure

Hello lammps developers,

I have a problem, I try to simulate a grafted nanoparticle is composed by
atomistic functional groups and rigid body for the np, in water solution.
So when a try to equilibrated in the npt ensemble the virial pressure not
fluctuate around the external pressure applied in the barostat.

# input lammps soft sphere magnetite nanoparticle grafted with alkane in
water/heptane interface
units real
atom_style full
boundary p p p

bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic

read_data equil_npt_np_water.data

pair_style hybrid soft/sphere lj/cut 1.0 lj/charmm/coul/long 8.5 10.0

pair_modify pair lj/charmm/coul/long tail yes

kspace_style pppm 0.0001

neighbor 2 bin
neigh_modify delay 0

group NP type 7 8
group grafted type 1 2 3 4 5 6
group water type 9 10
group solution union grafted water

timestep 0.5

thermo 1000
thermo_style custom step temp evdwl ecoul ebond eangle ke pe etotal press vol

compute stens all stress/atom NULL

reset_timestep 0
fix run_npt_solution solution npt temp 300 300 50 iso 1.0 1.0 5000 dilate all
fix run_npt_NP NP rigid/nvt group 1 NP temp 300 300 50
dump e_data all custom 2000 np_water.dat id type x y z c_stens[1]
c_stens[2] c_stens[3] c_stens[4] c_stens[5] c_stens[6]
dump_modify e_data format "%d %d %3.3f %3.3f 3\.3f .6e \.6e .6e \.6e .6e %.6e" sort id
run 2000000
unfix run_npt_solution
unfix run_npt_NP

write_data prod_npt_np_water.data

when I plot step vs pressure, I observe that the pressure fluctuate around
-150 atm, how is fix this problem, if will necessary I send the
topological lammps file (34M) is only send me a message.

Step Temp E_vdwl E_coul E_bond E_angle KinEng PotEng TotEng Press Volume
       0 299.75846 62676.669 2024430.4 45334.141 57245.897
  141811.93 -484103.68 -342291.75 -15.945547 1619560.8
    1000 299.56054 63559.814 2022943.3 45680.472 57224.075
   141718.3 -484302.48 -342584.18 -69.335057 1619651.2
    2000 300.03958 63451.315 2024009.3 45938.949 56979.01
  141944.93 -483368.72 -341423.79 -31.232467 1619879.7
    3000 300.02608 63344.531 2023793.3 45831.099 57117.621
  141938.54 -483608.09 -341669.55 -407.54307 1619997.7
    4000 299.28648 62846.062 2023992.6 45693.602 57155.627
  141588.64 -484050.65 -342462 -259.0037 1620094
    5000 300.42388 62916.116 2023699.4 45111.39 57238.472
  142126.74 -484777.83 -342651.09 -83.807339 1620138.5
    6000 300.19298 63050.402 2023898.5 45381.707 57384.566
   142017.5 -484042.88 -342025.39 37.874201 1619741.7
    7000 299.83189 62703.117 2024321 45490.468 57221.717
  141846.67 -484012.68 -342166.01 -220.86196 1618770
    8000 300.54022 64448.712 2021885.8 45564.507 57328.167
  142181.78 -484460.91 -342279.14 -54.182357 1617792.3
    9000 300.0973 63081.162 2023492.5 45650.163 57273.629
  141972.23 -484237.19 -342264.95 -353.75228 1617578.6
   10000 299.60592 63561 2023700.7 45592.064 57182.262
  141739.77 -483700.49 -341960.72 11.893554 1617920.7
   11000 300.81133 62862.142 2024698.9 45436.223 57109.614
  142310.03 -483641.27 -341331.24 106.3159 1618811.6
   12000 300.47735 62616.114 2024639.4 45144.49 57189.655
  142152.03 -484145.25 -341993.22 -63.810877 1619727.1
   13000 300.3735 63187.49 2024050.5 45490.264 57083.727
   142102.9 -483909.03 -341806.13 15.377146 1620501.2
   14000 299.77958 63040.573 2023707.7 45499.753 57050.742
  141821.93 -484436.63 -342614.71 -229.33338 1620844.4
   15000 299.58829 62902.536 2023634.2 45943.508 57298.246
  141731.43 -483977.81 -342246.39 -497.58872 1621122.1
   16000 300.14592 62913.348 2023487.5 45950.227 56945.861
  141995.23 -484410.63 -342415.39 -489.85013 1621075.1
   17000 299.90877 63320.285 2023901.5 45489.602 57042.477
  141883.04 -483979.57 -342096.53 -67.332023 1620848
   18000 300.89224 63623.765 2023460.9 45597.587 57111.714
  142348.31 -483921.16 -341572.85 265.36247 1620337.5
   19000 299.81027 62803.945 2024577.6 45194.902 57095.012
  141836.44 -484066.19 -342229.75 39.513341 1620071.9
   20000 300.3789 63275.139 2022873.2 45969.242 57705.433
  142105.45 -483934.98 -341829.53 -395.64175 1620304.1
   21000 299.53002 63454.214 2023303.9 45649.593 56879.587
  141703.86 -484421.81 -342717.95 -336.59007 1621205.7
   22000 299.0422 63135.141 2024177.9 45427.739 57216.697
  141473.08 -483776.78 -342303.7 -203.43387 1622333

1997000 300.19545 63325.534 2023404.7 45770.832 57101.044
  142018.67 -484107.44 -342088.77 -276.68097 1616351.2
1998000 299.26005 62825.127 2024106.9 45897.162 57018.648
  141576.14 -483866.32 -342290.18 -446.33792 1617175
1999000 299.68923 63290.039 2023400.2 45277.471 56958.161
  141779.18 -484742.6 -342963.42 -2.0341001 1617923.7
2000000 301.47741 62986.927 2024100.6 45429.623 56999.678
  142625.15 -484219.81 -341594.66 133.9922 1618602.1
Loop time of 176668 on 64 procs (64 MPI x 1 OpenMP) for 2000000 steps with
159019 atoms

Pair time (\) = 96231 \(54\.47\) Bond time \() = 871.232 (0.493147)
Kspce time (\) = 29226\.3 \(16\.5431\) Neigh time \() = 19179.6 (10.8563)
Comm time (\) = 24127\.3 \(13\.6569\) Outpt time \() = 95.7859 (0.0542181)
Other time (%) = 6936.59 (3.92635)

Thanks
Samuel

in.npt-np-water (5.55 KB)

log.lammps (282 KB)

Hello lammps developers,

I have a problem, I try to simulate a grafted nanoparticle is composed by
atomistic functional groups and rigid body for the np, in water solution.
So when a try to equilibrated in the npt ensemble the virial pressure not
fluctuate around the external pressure applied in the barostat.

have you checked what are the virial contribution from the internal
interactions of your nanoparticle.
due to using fix rigid its internal forces are projected out and its
positions not updated. so if those have a significant contribution to
the total virial, this can put things off balance.

you can try, e.g. neigh_modify exclude group NP NP

timestep may be an issue, too, depending on the shape of your rigid body.

axel.

axel.

Hello lammps developers,
In my case the rigid nanoparticle is conform by a central particles and
174 beads particles uniformly distributed at distance R (to emulated a
sphere), in this case the beads interacting by a lj/charmm/coulomb/long
pair potential with the grafted particles and the solution, the NP
interacting by a shifted potential to repel all particle at distance R, so
I don't know if can exclude the interacting potential of the NP group with
the other particles. Thank you for you help me.

Thanks
Samuel

Hello lammps developers,
In my case the rigid nanoparticle is conform by a central particles and
174 beads particles uniformly distributed at distance R (to emulated a
sphere), in this case the beads interacting by a lj/charmm/coulomb/long
pair potential with the grafted particles and the solution, the NP
interacting by a shifted potential to repel all particle at distance R, so
I don't know if can exclude the interacting potential of the NP group with
the other particles. Thank you for you help me.

that is not what i suggested. look up the docs for neigh_modify and
study carefully what the option i suggested to you does.

axel.