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Re: [lammps-users] Selecting the accuracy parameter for pppm
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Re: [lammps-users] Selecting the accuracy parameter for pppm

From: Steve Plimpton <sjplimp@...24...>
Date: Wed, 2 May 2018 08:57:51 -0600

Stan (CCd) might have thoughts on this.


On Sun, Apr 29, 2018 at 8:45 PM, Pengyu Huang <> wrote:

Dear all,

I am modeling the flexible water and flexible co2 placed in between two silica surfaces, with periodic boundary conditions at x-axis and y-axis and non-periodic boundary at z-axis (perpendicular to the silica surfaces). I am looking at the contact angles for the three phases system. The timestep was chosen as 0.25 fs.  Both cuts off of LJ and Coulomb interactions are 12 Angstroms. The long-range Coulomb forces are calculated with pppm and with " kspace_modify slab 3.0 ". 

I have relaxed the system at 0.5 ns with Langevin and another 0.5 ns with nose-hoover thermostat with pppm 1e-6, with damping time of 50 fs. Then I have tested with different accuracy parameters of pppm in the NVE ensemble for 50 ps: 1e-4, 1e-5 and 1e-6. Using accuracy of 1e-5 is approximately 2 times faster than with 1e-6, but it gives a very small energy drift (see attached).  I have calculated the ratio of root-mean-square fluctuations of energy to the averaged energy of the system, which is 3.8 e-7. I think this value is quite low. I have also attached individual plots of energy vs time for simulations with "pppm 1e-5" and "pppm 1e-6", although the one with "pppm 1e-6" has not finished yet.

The whole simulations would need around 10 ns for measuring the contact angle, according to the literature. Using "pppm 1e-6" would need around 4 months for my system (around 100,000 atoms) at a computational node with 32 cores, although I have seen someone using an accuracy parameter of 1e-4 and with a larger timestep. Should I be worried about the small energy drift if I am choosing the accuracy parameter of 1e-5 and running the simulation under nose-hoover thermostats? If I have to stick with "pppm 1e-6",  are there any other methods to speed up the simulations?  I have tried the r-RESPA for calculating the kspace at every 1fs which can speed up to around 2 times for "pppm 1e-6". Varying the cut off of Coulomb interactions would not help much. I also want to calculate correct pressure so I did not try pppm/stagger.

Thank you for your time.


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