NMMD / MDSPACE -- Extension of GENESIS 2.1

Installation:

See https://www.r-ccs.riken.jp/labs/cbrt/installation/ for installation requirements

To build GENESIS :

cd /path/to/genesis
autoreconf -fi
./configure
make install

Usage NMMD:

The input file is similar as in GENESIS (see how to define the input file in https://www.r-ccs.riken.jp/labs/cbrt/usage/). To use NMMD, you must chose the integrator=NMMD in the DYNAMICS section and add a section NMMD to the INP file as follow :

...

[DYNAMICS]
integrator = NMMD

...

[NMMD]
nm_number = 10
nm_mass = 10.0
nm_file = /path/to/nm/file
nm_dt = 0.001

• nm_number : The number of normal modes to use after skipping the 6 first modes (example : 10 will use modes from 7-16), default 10
• nm_mass : Mass value of Normal modes for NMMD, default : 10.0
• nm_file : file containing the normal mode vectors
• nm_dt : normal mode integration time step, default :0.001

Limitations:

• NMMD is available only for ATDYN
• NMMD is available only for LANGEVIN temperature control in the NVT enemble
• SHAKE/RATTLE algorithm have to be turn off

Usage MDSPACE:

The MDSPACE extension allows to fit images instead of volumes

usage :

[EXPERIMENTS]
emfit = YES                            # YES/NO
emfit_type = IMAGE                     # VOLUME/IMAGE 
emfit_target = path/to/image/file.spi  # 2D SPIDER file
emfit_sigma = 2.0                      # sigma of 2D gaussian
emfit_tolerance = 0.01                 # Gaussian truncation threshold
emfit_period = 1                       # not used
emfit_roll_angle = 0.0                 # Euler roll angle in degrees
emfit_tilt_angle = 0.0                 # Euler tilt angle in degrees
emfit_yaw_angle = 0.0                  # Euler yaw angle in degrees
emfit_shift_x = 0.0                    # Shift in x direction in pixels
emfit_shift_y = 0.0                    # Shift in y direction in pixels
emfit_pixel_size = 1.0                 # Size of a pixel in Angstrom

Limitations:

• NMMD is available only for ATDYN

genesis-2.0

Source code for genesis 2.0 beta for Fugaku For GENESIS compile on Fugaku and execution, please see READMD.howto