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
- 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
- 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
- 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, since
individual lambda windows cannot span multiple GPUs but
one GPU can run multiple windows provided sufficient GPU memory is available.
Constant pH Molecular Dynamics
Constant pH molecular dynamics simulations can run with the Generalized Born implicit solvent
model and with explicit solvent as described in the manual and
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):
|ibelly != 0
||Simulations using belly style constraints are not supported.
|(igb != 0 & cut < systemsize)
||GPU accelerated implicit solvent GB simulations do not support a
|nmropt > 1
||Support is not currently available for nmropt > 1. In addition, for
nmropt = 1, only features that do not change the underlying force field parameters are
supported. For example umbrella sampling restraints are supported as well as simulated
annealing functions such as variation of Temp0 with simulation step. However, varying the
VDW parameters with step is NOT supported.
|nrespa != 1
||No multiple time stepping is supported.
|vlimit != -1
||For performance reasons the vlimit function is not implemented on
|es_cutoff != vdw_cutoff
||Independent cutoffs for electrostatics and van der Waals are not
supported on GPUs. (Although it may be coming.)
|order != 4
||A PME interpolation order of 4 is the only option supported. Currently
we do not see an advantage in making a tradeoff between mapping work and FFT reduction, nor
an advantage in trading direct space electrostatics for reciprocal space work.
|imin = 1 (in parallel)
||Minimization is only supported in the serial GPU code, and it is wise to
use the double-precision form of the code at that. Highly strained systems may need to be
minimized using the CPU code.
|emil_do_calc != 0
||Emil is not supported on GPUs.
|isgld > 0
||Self guided langevin is not supported on GPUs.
|iemap > 0
||EMAP restraints are not supported on GPUs.
|icfe > 0 & imin > 0
||Minimization is not supported for TI/MBAR on GPUs.
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.