GENESIS 1.2.1 released

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)

GENESIS 1.2.0 released!

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).

GENESIS 1.1.6 released

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

GENESIS tutorial in Japanese at Tokyo (Oct. 5, 2017)

(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。

GENESIS 1.1.5 released!

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

GENESIS 1.1.4 released

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

GENESIS 1.1.3 released

This version is an urgent bugfix version. Users of 1.1.2 must update to this version.

Fixes:

  • (spdyn) fix bug of contact_check when OpenMP thread number > 1 (not always)