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GPU Features of Interest in Amber18

The GPU accelerated version of PMEMD 18 supports both explicit solvent PME or IPS simulations in all three canonical ensembles (NVE, NVT and NPT) and implicit solvent Generalized Born simulations. It has been designed to support as many of the standard PMEMD v18 features as possible, however, there are some current limitations that are detailed below. Some of these may be addressed in the near future, and patches released, with the most up to date list posted on the web page.

Alchemical Free Energy Calculations
The free energy methods implemented in Amber18 GPU code builds on the efficient AMBER GPU MD code base (pmemd.cuda). These methods include both thermodynamic integration and free energy perturbation (FEP) and multi-state Bennett’s ratio (MBAR) classes.

• Thermodynamic Integration (TI): The input flags to run a TI calculation on a GPU are the same as for the CPU version. Users need to:
  • Set icfe=1 : to enable the free energy calculations
  • Define perturbated regions in timask1, timask2
  • Set ifsc=1 : to utilize the soft-core potentials
  • Define softcore regions in scmask1, scmask2
  • Define the current alchemical progress variable lambda by setting clambda.
  • There is a CPU-version tutorial available and users can run it with the GPU version without any modification in the input.
• FEP/MBAR: To generate additional output info for subsequent FEP/MBAR analysis:
• Users first need to define TI input flags as above
• Enable the FEP/MBAR output: ifmbar=1
• Define the number of MBAR states in mbar_states, e.g., mbar_states=11
• Specify the lambda value of each MBAR stat, e.g. mbar_lambda = 0.0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1.0,
• Define the MBAR output interval, bar_intervall, e.g. bar_intervall=10 means AMBER will output MBAR results every 10 MD steps

Replica-Exchange Molecular Dynamics
Similar to Amber16, Amber18 is capable of performing temperature, Hamiltonian, and pH replica exchange simulations on the GPU. Multi-dimensional replica exchange simulations, where two or more conditions are simulated at the same time, are supported as well. The details of input and control variables can be found in both the Amber16 and Amber18 manuals. The newly implemented free energy methods in Amber18 can be performed in conjunction with Hamiltonian replica exchange so that different windows can exchange their conformations. To enable such calculations, users need to:

• Create input files for all lambda values.
• Define Hamiltonian replica exchange input flags in each input file
• numexchg: the number of exchange attempts that will be performed between replica pairs
• nstlim: the number of MD steps that will be performed between exchange attempts
• Define the Hamiltonian replica exchange group file. Note that:
• In the group file, the entries must be sorted according to the lambda values
• Currently, the number of entries in the group files must be the same as the number of lambda windows.
• Currently, the number of lambda windows must be a multiple of the available GPUs, e.g., if there are 12 lambda windows, users need to allocate 1, 2, 3, 4, 6, or 12 GPUs. That is, free energy simulations of individual lambda window cannot be executed on multiple GPUs but one GPU can run multiple windows, provided sufficient GPU memory is available.

Constant pH Molecular Dynamics
A constant pH molecular dynamics simulations can run with the Generalized Born implicit solvent model and with explicit solvent, as details are described in the manual and there is an online tutorial available.

While we aim to port as many useful features as possible to the GPU, the project is not yet complete and we have also declined to support some protcols in the interest of steering the community away from bad ideas. The following options are NOT supported (as of the AMBER GPU v18.0.0 release):

An important new default feature
One important change in AMBER 18 is that netfrc is now computed when running on GPUs. Prior to Amber18 the behavior was to skip netfrc calculation regardless of the setting of netfrc in &ewald. Amber18 now respects the netfrc setting so the default behavior, in the absence of netfrc in the &ewald namelist, will be to calculate netfrc.

Minor changes in the output since Amber16
There are some minor differences in the output format. For example, the Ewald error estimate is NOT calculated when running on a GPU. We have updated the Amber18 outputs and test cases to reflect this fact--Amber16 and earlier versions printed the CPU-based Ewald error estimate, but this was a meaningless report. The error estimate coming out of the CPU pertains to the error in the spline approximation of the Ewald direct space force and energy, a spline-based approximation to terms based on erfc(). In Amber18, the GPU also uses a spline-based approximation to obtain the Ewald direct space force between particles, but the splines are in fact more accurate than analytic computation in 32-bit floating point arithmetic due to the way we tweak the coefficients when fashioning them on the CPU for use by the kernels. We do not calculate the error due to this process, but rest assured the direct sum tolerance and aliasing effects on the grid are much worse for the numerics than the spline will be.