Currently calculation of the full pressure tensor in MSM is expensive. -Using the kspace_modify -pressure/scalar yes command provides a less expensive way to compute the -scalar pressure (Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example, -to run an isotropic barostat. If the full pressure tensor is needed, then -calculating the pressure at every timestep or using a fixed pressure -simulation with MSM will cause the code to run slower. +Using the kspace_modify pressure/scalar yes +command provides a less expensive way to compute the scalar pressure +(Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example, +to run an isotropic barostat. If the full pressure tensor is needed, +then calculating the pressure at every timestep or using a fixed +pressure simulation with MSM will cause the code to run slower.
Note that style pppm only computes the grid size at the beginning of -a simulation, so if the length or triclinic tilt of the simulation cell -increases dramatically during the course of the simulation, the accuracy -of the simulation may degrade. For example, for a triclinic system with -all three tilt factors set to the maximum limit, the PPPM grid should be -increased roughly by a factor of 1.5 in the y direction and 2.0 in the z -direction as compared to the same system using a cubic orthogonal simulation -cell. One way to ensure the accuracy requirement is being met is to run a -short simulation at the maximum expected tilt or length, note the required -grid size, and then use the kspace_modify mesh -command to manually set the PPPM grid size to this value. +a simulation, so if the length or triclinic tilt of the simulation +cell increases dramatically during the course of the simulation, the +accuracy of the simulation may degrade. Likewise, if the +kspace_modify slab option is used with +shrink-wrap boundaries in the z-dimension, and the box size changes +dramatically in z. For example, for a triclinic system with all three +tilt factors set to the maximum limit, the PPPM grid should be +increased roughly by a factor of 1.5 in the y direction and 2.0 in the +z direction as compared to the same system using a cubic orthogonal +simulation cell. One way to ensure the accuracy requirement is being +met is to run a short simulation at the maximum expected tilt or +length, note the required grid size, and then use the +kspace_modify mesh command to manually set the +PPPM grid size to this value.
RMS force errors in real space for ewald and pppm are estimated using equation 18 of (Kolafa), which is also referenced as diff --git a/doc/kspace_style.txt b/doc/kspace_style.txt index c675bb4f92..911e34c013 100644 --- a/doc/kspace_style.txt +++ b/doc/kspace_style.txt @@ -193,12 +193,12 @@ angstroms instead of 10 angstroms) provides better MSM accuracy for both the real space and grid computed forces. Currently calculation of the full pressure tensor in MSM is expensive. -Using the "kspace_modify"_kspace_modify.html -{pressure/scalar yes} command provides a less expensive way to compute the -scalar pressure (Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example, -to run an isotropic barostat. If the full pressure tensor is needed, then -calculating the pressure at every timestep or using a fixed pressure -simulation with MSM will cause the code to run slower. +Using the "kspace_modify"_kspace_modify.html {pressure/scalar yes} +command provides a less expensive way to compute the scalar pressure +(Pxx + Pyy + Pzz)/3.0. The scalar pressure can be used, for example, +to run an isotropic barostat. If the full pressure tensor is needed, +then calculating the pressure at every timestep or using a fixed +pressure simulation with MSM will cause the code to run slower. :line @@ -216,16 +216,20 @@ to determine the number of K-space vectors for style {ewald} or the grid size for style {pppm} or {msm}. Note that style {pppm} only computes the grid size at the beginning of -a simulation, so if the length or triclinic tilt of the simulation cell -increases dramatically during the course of the simulation, the accuracy -of the simulation may degrade. For example, for a triclinic system with -all three tilt factors set to the maximum limit, the PPPM grid should be -increased roughly by a factor of 1.5 in the y direction and 2.0 in the z -direction as compared to the same system using a cubic orthogonal simulation -cell. One way to ensure the accuracy requirement is being met is to run a -short simulation at the maximum expected tilt or length, note the required -grid size, and then use the "kspace_modify"_kspace_modify.html {mesh} -command to manually set the PPPM grid size to this value. +a simulation, so if the length or triclinic tilt of the simulation +cell increases dramatically during the course of the simulation, the +accuracy of the simulation may degrade. Likewise, if the +"kspace_modify slab"_kspace_modify.html option is used with +shrink-wrap boundaries in the z-dimension, and the box size changes +dramatically in z. For example, for a triclinic system with all three +tilt factors set to the maximum limit, the PPPM grid should be +increased roughly by a factor of 1.5 in the y direction and 2.0 in the +z direction as compared to the same system using a cubic orthogonal +simulation cell. One way to ensure the accuracy requirement is being +met is to run a short simulation at the maximum expected tilt or +length, note the required grid size, and then use the +"kspace_modify"_kspace_modify.html {mesh} command to manually set the +PPPM grid size to this value. RMS force errors in real space for {ewald} and {pppm} are estimated using equation 18 of "(Kolafa)"_#Kolafa, which is also referenced as