This version contains following bugfixes.
- (spdyn/atdyn) Enable generalized replica exchange with solute tempering (gREST)
- (spdyn) Improvement of nonbonded energy in GPU usage
- (spdyn/atdyn) Enable options, pressure_virial/pressure_rmsd,including virial terms from position/rmsd restraints in pressure evaluations
- (spdyn) Fix setup of AMBER FF when constraint is not set
- (atdyn) Fix PC restraints for computational performance
This version contains following bugfixes.
- (spdyn) Fix constraints on minimization
- (atdyn) Fix dispersion correction for AMBER FF
- (atdyn/spdyn) Fix memory allocation bug in off-grid REUS (if # of restraints in off-grid REUS > # of replicas)
- (general) extend maximum characters per line in control file (for recent CHARMM-GUI)
This version has the following new feature.
- (spdyn) TIP4P water model enabled (AMBER/CHARMM)
Fixes:
- (spdyn) minor bugfixes on domain specification
- (atdyn/spdyn) minor fixes for rpath parameters
- (build) support parallel compilation (e.g. make -j4)
- (build) enable_debug=4 enabled for gfortran
In addition, source tree is modified and the location of “./configure” has changed (genesis-1.2.0/configure).
We will give GENESIS seminars in SC17 at Denver as follows.
General introduction of GENESIS
by Dr. Chigusa Kobayashi (RIKEN, AICS)
on 14th Nov. AM11:00-11:10
High performance scheme in GENESIS
by Dr. Jaewoon Jung (RIKEN, AICS)
on 14th Nov. AM11:10-11:20
Come and join us!
This version contains several bugfixes.
Fixes:
- (spdyn) fix of GPU code for newer NVIDIA drivers (version > 380)
- (configuration) fix of configure files
- (atdyn/spdyn) enable restarting minimization
- (atdyn) nonb_limiter is enabled
(This is a GENESIS tutorial in Japanese)
2017/9/29 追記: 定員に達したため、参加受付を終了しました。
2017/10/5(木)に日本語でのGENESISチュートリアルを開催いたします。このチュートリアルはCBI学会2017年大会(2017/10/3-5, 東京)内のイベントとして行われます。アナウンスや申込み方法についてはこのCBI年次大会内の説明ページをご参照下さい。
詳細については順次このページに更新する予定です。
(2017/10/2 追記) 資料をアップロードしました。
This version contains a new feature and some fixes as follows.
New feature:
- (atdyn/spdyn) Fitting method (used in targeted MD, steered MD, string method etc.) renewal; [FITTING] section is introduced to extend the capability of structure fitting.
- (spdyn) improve GPU detection mechanism (automatically ignore GPUs with CC < 3.5)
Fixes:
- (atdyn/spdyn) Fix of R-path (string method)
- (atdyn/spdyn) fix random generator used in BUSSI thermostat/barostat
- (spdyn) fix for communication tag
- (spdyn/tests) update of BUSSI NVT (regression test is also updated)
- (atdyn/spdyn) fix of gromacs input for SMOG2
- (atdyn/spdyn) fix of restart file reader (K-computer and FX100 only; there could be large delay when reading input files (not always))
- (tests) test.py script now accepts relative path for the atdyn/spdyn executables
Presentation slides and materials used in the tutorial (Feb. 27-Mar. 1) are now available here.
This version is also an urgent bugfix release. Users of 1.1.2/1.1.3 must update to this version.
Fixes:
- (spdyn) additional fix for OpenMP
