[gmx-users] k-space settings in GROMACS

[Mark Abraham]

Hi,

On Wed, 18 Mar 2020 at 07:02, Anh Vo <atv55 at msstate.edu> wrote:

> Hi everyone,
>
> I'm trying to reconstruct in GROMACS some LAMMPS simulation to compare
> between the two. I'm simulating a lipid bilayer system with 72 POPC lipids
> and 9072 water molecules, as well as a single lipid system (1 POPC
> molecule) and water only system (100 H2O molecules).
>

Start with a simpler system when proving you understand how to set up
equivalent simulations.

I try to use the same settings in GROMACS as in LAMMPS. However, in LAMMPS
> I have *kspace_style* to define a long-range solver and *kspace_modify* to
> set
> parameters used by the kspace solvers; but I'm not sure which command I
> should use for similar settings in GROMACS. (I have read the manual and
> searched online but haven't figured it out. Please accept my apology if
> this seems to be an obvious question).
>
> In details, these 2 commands in LAMMPS are:
> *  - kspace_style    pppm  1e-5   *(pppm is P3M algorithm, 1.0e-5 means
> that the RMS error will be a factor of 100,000 smaller than the reference
> force)
>

Then you'll know that ewald_rtol does exactly that, and that
http://manual.gromacs.org/documentation/current/user-guide/mdp-options.html#mdp-value-coulombtype=P3M-AD
does
what you want.

*  - kspace_modify   diff  ad    *(*diff*  keyword specifies the
> differentiation scheme used by the PPPM method to compute forces on
> particles,  *ad*  keyword means approach uses only 1 FFT to transfer
> information back to real space for a total of 2 FFTs per timestep).
>
> Please help me to get similar settings in GROMACS (e.g. which command
> should I use ?). Also, would it make a significant difference (e.g. in the
> energy of the molecules, in the output pressure, etc.) if I use PME instead
> of PPPM in GROMACS ?
>

No need to do that.

Mark


> Thank you very much for your help.
>
> Best,
> Anh Vo
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