TIP5P with OPLSAA ethanol mixure, error:Non-numerical pressure-simulation unstable

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#1

Dear Andrew

I tested the recommended scripts for the binary mixture of TIP5P/TIP4P/TIP3P water with OPLSAA ethanol one by one and the result are attached in this eamil. For TIP5P water+OPLSAA ethanol, these three methods listed below can converge to the right results. But systems performed by some other methods seems to expand continually which is odd and i still can not figure it out.

Method 4
fix fxH2O H2O rigid/nph/small molecule iso 1 1 1000 dilate all
fix fxEthanol ethanol nve
fix fxLanvegin all langevin 298 298 100.0 48279
Correct

Method 5
fix fxH2O H2O rigid/npt/small molecule temp 298 298 100 iso 1 1 1000 dilate all
fix fxEthanol ethanol nve
Correct

Method 8
fix fxH2O H2O rigid/nph/small molecule iso 1 1 1000
fix fxEthanol ethanol nve
fix fxLanvegin all langevin 298 298 100.0 48279
Correct

Here is the detailed explanation for hybrid simulation with rigid and non-rigid particles i found in lammps mannual:

If you with to perform NPT or NPH dynamics (barostatting), you cannot use both fix npt and the NPT or NPH rigid styles. This is because there can only be one fix which monitors the global pressure and changes the simulation box dimensions. So you have 3 choices:

Use one of the 4 NPT or NPH styles for the rigid bodies. Use the dilate all option so that it will dilate the positions of the non-rigid particles as well. Use fix nvt (or any other thermostat) for the non-rigid particles.
Use fix npt for the group of non-rigid particles. Use the dilate all option so that it will dilate the center-of-mass positions of the rigid bodies as well. Use one of the 4 NVE or 2 NVT rigid styles for the rigid bodies.
Use fix press/berendsen to compute the pressure and change the box dimensions. Use one of the 4 NVE or 2 NVT rigid styles for the rigid bodies. Use fix nvt (or any other thermostat) for the non-rigid particles.
In all case, the rigid bodies and non-rigid particles both contribute to the global pressure and the box is scaled the same by any of the barostatting fixes.

Best regards
Yalishanda

------------------ Original ------------------

TIP3P+OPLSAA.txt (872 Bytes)

TIP4P+OPLSAA.txt (1.04 KB)

TIP5P+OPLSAA0730.txt (1.17 KB)

#2

> > >> A word of caution about the rigid TIP5P - flexible ethanol system
> > >> mentioned below.

https://github.com/jewettaij/moltemplate/tree/master/examples/all_atom/force_field_OPLSAA/waterTIP5P%2Bethanol

> > >> While relatively short runs went OK, longer ones
> > >> inevitable ended up in crashes even when I reduced the time step to 1 fs
> > >> from the original 2 fs.

I believe you that 2fs is too large. I'm not certain about 1fs.
I ran a 4.5e+06 iterations simulation using a 1fs timestep under NVE
conditions. The total energy of the system drifted by about 0.5%
after 100000 iterations (3.5% in 1000000 iterations).

I also ran an NPT simulation for 1e+06 simulations using a 1fs
timestep without running into issues.
(other than the fact that the ethanol and water phase-separated.
Weird. I'll worry about that another day.)
Perhaps I should have run that one longer.

Either way, I was unable to reproduce any obvious problems using a 1fs
timestep when running the simulation overnight. But I will change the
example to use a 0.5fs timestep to be on the safe side.

Thanks for letting me know about this

Andrew