NAMD 2.11 New Features
Released in NAMD 2.11
The following features have been released in NAMD 2.11.
Any bug fixes will appear in the nightly build version on the
Any documentation updates will appear in the Nightly Build User's Guide
and release notes.
GPU-accelerated simulations up to twice as fast as NAMD 2.10
For example, on a dual E5-2680 v3 workstation with two GTX 980 GPUs
the 92K-atom ApoA1 benchmark drops from 12.2 ms/step to 5.6 ms/step
while the 1.06M-atom STMV benchmark drops from 79 ms/step to 57 ms/step.
The largest performance increases are for implicit solvent simulations or
runs that output energy on every timestep.
Enhanced Tcl scripting of collective variables and "cv" command
Collective variables module improvements including to histogram bias
TclForces query total net forces for atom groups
Replica-exchange multiplexing (fewer partitions than replicas)
New asynchronous inter-replica communication commands (described below)
enable an arbitrary number of "logical" replicas to be multiplexed
onto a smaller number of "physical" replical partitions. In short, the
+replicas argument no longer needs to match the num_replicas variable,
and replica exchange can be performed even on multicore builds.
Multiplexing reduces the impact of performance differences between replicas
and avoids synchronizing writes to output files.
Multiplexed replica exchange is implemented in the new "multiplex.namd" script
and uses the same configuration files as the still valid "replica.namd" script.
Tcl scripting multiple in-memory checkpoints
The new commands checkpointStore, checkpointLoad, checkpointSwap, and checkpointFree
take a string key argument, by which checkpoints are distinguished.
Improved Tcl scripting multi-copy interface documentation
Tcl scripting asynchronous multi-copy remote in-memory checkpoints
The new checkpointStore/Load/Swap/Free commands take an optional second argument that
is either the target replica on which to store the checkpoint or the keyword "global".
Tcl scripting asynchronous multi-copy remote trajectory output
The new command "replicaDcdFile index ?filename?
" opens a trajectory
file that is written to by any replica that uses the same index.
Tcl scripting asynchronous multi-copy remote script evaluation
The new command "replicaEval replica script
asynchronously executes its script in the top-level context of the target replica's Tcl interpreter and
returns the result or error.
Tcl scripting asynchronous multi-copy central work queue support
See the enqueue_work and schedule_work procedures in the new "multiplex.namd" script.
Tcl scripting asynchronous multi-copy workflow-style programming
See the dependent_work and dependent_set procedures in the new "multiplex.namd" script.
Improved minimization for Drude force field and rigid bonds
Rigid bonds and Drude hard-wall constraints are now enforced during minimization.
Fix long-range LJ correction for systems larger than 11,000 atoms
An integer overflow in "16*numatoms*numatoms" resulted in the VDW tail correction
(which is off by default) being too small and possibly of the wrong sign
for all but the smallest systems, with the magnitude of the applied (incorrect)
correction declining as system volume increased, as if no correction was applied.
Improved long-range LJ correction with VDW force switching
Improved alchemical calculations with VDW force switching
Pressure calculation with fixed atoms on GPU works as on CPU
Improved scaling for GPU-accelerated particle-mesh Ewald calculation
CPU-side operations overlap better and are parallelized across cores.
Improved scaling for GPU-accelerated simulations
Nonbonded force calculation results are streamed from the GPU for better overlap.
Improved scaling for multi-threaded "smp" builds
Prevent running smp builds with one thread per process
Support trajectory files larger than 2GB on Windows
NVIDIA CUDA GPU-acceleration binaries for Mac OS X
Improved Intel Xeon Phi coprocessor support
Update to Charm++ 6.7.0 with improved multi-copy support
Ignore ioformat statement in CHARMM topology and parameter files
Psfgen improvements including long resids and insertion codes
Psfgen package available in NAMD Tcl interpreter
Similar to VMD, "package require psfgen" will make psfgen commands available in a NAMD config file
to enable building and running a structure in a single Tcl interpreter.
NAMD and psfgen do not share data structures and must communicate via files.