Input File Template Generation

GENESIS executables (atdyn, spdyn, and various analysis tools) can generate template input files when special argument is specified. List of available special arguments can be shown by running command without arguments. For example, spdyn will show the following message.

% ./spdyn 
# normal usage
% mpirun -np XX ./spdyn INP
# check control parameters of md
% ./spdyn -h ctrl md
# check control parameters of min
% ./spdyn -h ctrl min
# check control parameters of remd
% ./spdyn -h ctrl remd
# check control parameters of rpath
% ./spdyn -h ctrl rpath
# check all control parameters of md
% ./spdyn -h ctrl_all md
# check all control parameters of min
% ./spdyn -h ctrl_all min
# check all control parameters of remd
% ./spdyn -h ctrl_all remd
# check all control parameters of rpath
% ./spdyn -h ctrl_all rpath

spdyn has several run modes (md, min, remd, and rpath). Please note that the input file formats of the energy minimization, MD, and REMD are different. Input file template for each run type can be obtained by appending corresponding command line argument. If you wanna know the general input parameters of MD simulation, ./spdyn -h ctrl md may be appropriate. If you wanna know all the available parameters, use -h ctrl_all instead of -h ctrl. Template input file of basic MD looks like this.

For another example, wham_analysis will show this simple message.

% ./wham_analysis 
# normal usage
% ./wham_analysis INP
# usage to see control parameters
% ./wham_analysis -h ctrl

Template input file of wham_analysis can be saved by executing ./wham_analysis -h ctrl.

$ /home/user/genesis/bin/wham_analysis -h ctrl > INP
$ more INP
# control parameters in wham_analysis
psffile        = input.psf # protein structure file
prmtopfile     = # AMBER parameter topology file
ambcrdfile     = input.crd # AMBER coordinate file
grotopfile     = # GROMACS topology file
grocrdfile     = input.crd # GROMACS coordinate file
pdbfile        = input.pdb # PDB file
dcdfile        = input{}.dcd # DCD file
cvfile         = input{}.cv # Collective variable file
pmffile        = output.pmf # potential of mean force file
dimension      = 1
nblocks        = 1
temperature    = 300.0
tolerance      = 10E-08
rest_function1 = 1
grids1         = 0.0 360.0 91 # min max num_grids, num_grids means the number of bins + 1

group1         = an:NL
group2         = an:CA
group3         = an:CRP
group4         = an:NR

function1      = DIHED
select_index1  = 1 2 3 4
constant1      = 1.0 1.0 1.0 1.0
reference1     = 144.0 146.0 148.0 150.0
is_periodic1   = YES
box_size1      = 360.0

Other tools can also generate such input template file.