PLUMED-NEST

Project ID: plumID:21.048
Source: plumed3.dat
Originally used with PLUMED version: 2.5
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

# plumed input for metadynamics amber prod run 

# restart simulation (switch on after the first run to continue runs -reading from and appending to existing COLVAR and HILLS files)
#RESTART

# change distance/position units of I/O to Angstroms (default nm)
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A


# define virtual atom for centre of mass of lidocaine (=39atoms incl. H)
The UNITS action with label  calculates somethinglqzThe COM action with label lqz calculates the following quantities:
 Quantity   
 Type   
 Description  
lqz
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=18531-18569

# define COM for point at base of vertical pore axis using CAatoms of 4x2x3 residues at bottom of each s5/6
ax_baseThe COM action with label ax_base calculates the following quantities:
 Quantity   
 Type   
 Description  
ax_base
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=2222,2239,2258,4418,4437,4456,7107,7121,7140,8594,8613,8633,11313,11332,11351,13359,13378,13398,16676,16683,16702,18275,18292,18313

# define COM for point at top of vertical pore axis using CA of 4x6 residues on each P1
ax_topThe COM action with label ax_top calculates the following quantities:
 Quantity   
 Type   
 Description  
ax_top
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3631,3641,3661,3680,3690,3709,7862,7873,7893,7912,7931,7947,12427,12434,12455,12474,12485,12504,17299,17310,17329,17348,17359,17378

# define COM for point to define the transverse axis using CA of 2x6 residues on P1 of DI/DII
ax_sideThe COM action with label ax_side calculates the following quantities:
 Quantity   
 Type   
 Description  
ax_side
atoms
virtual atom calculated by COM action: COMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=3631,3641,3661,3680,3690,3709,7862,7873,7893,7912,7931,7947

# Calculate distances of vectors between coms
d_axThe DISTANCE action with label d_ax calculates the following quantities:
 Quantity   
 Type   
 Description  
d_ax
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ax_top,ax_base
dtop_lqzThe DISTANCE action with label dtop_lqz calculates the following quantities:
 Quantity   
 Type   
 Description  
dtop_lqz
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ax_top,lqz
dbase_lqzThe DISTANCE action with label dbase_lqz calculates the following quantities:
 Quantity   
 Type   
 Description  
dbase_lqz
scalar
the DISTANCE between this pair of atoms: DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=ax_base,lqz


# Calculate position based on the projection along the vertical pore axis
zThe CUSTOM action with label z calculates the following quantities:
 Quantity   
 Type   
 Description  
z
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dtop_lqz,dbase_lqz,d_ax FUNCthe function you wish to evaluate=(0.5*(y^2-x^2)/z) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# Calculate perpendicular distance of lqz from the vertical pore axis
rThe CUSTOM action with label r calculates the following quantities:
 Quantity   
 Type   
 Description  
r
scalar
an arbitrary function: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=dtop_lqz,d_ax,z VARthe names to give each of the arguments in the function=x,z,o FUNCthe function you wish to evaluate=(sqrt(x^2-(z/2-o)^2)) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO

# Calculate third positional parameter using torsional angle 
thetaThe TORSION action with label theta calculates the following quantities:
 Quantity   
 Type   
 Description  
theta
scalar
the TORSION involving these atoms: TORSIONCalculate one or multiple torsional angles. More details AXIStwo atoms that define an axis=ax_top,ax_base VECTOR1two atoms that define a vector=ax_top,ax_side VECTOR2two atoms that define a vector=ax_base,lqz


# Add bias restraints to lqz position along s and z so it does not leave the pore interior
ruwallThe UPPER_WALLS action with label ruwall calculates the following quantities:
 Quantity   
 Type   
 Description  
ruwall.bias
scalar
the instantaneous value of the bias potential
ruwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=r ATthe positions of the wall=18.0 KAPPAthe force constant for the wall=100 EXP the powers for the walls=2
rlwallThe LOWER_WALLS action with label rlwall calculates the following quantities:
 Quantity   
 Type   
 Description  
rlwall.bias
scalar
the instantaneous value of the bias potential
rlwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=r ATthe positions of the wall=0.0 KAPPAthe force constant for the wall=100 EXP the powers for the walls=2 # Should not be necessary; but might help prevent GPU errors ?
zlwallThe LOWER_WALLS action with label zlwall calculates the following quantities:
 Quantity   
 Type   
 Description  
zlwall.bias
scalar
the instantaneous value of the bias potential
zlwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: LOWER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=z ATthe positions of the wall=-12.0 KAPPAthe force constant for the wall=100 EXP the powers for the walls=2
zuwallThe UPPER_WALLS action with label zuwall calculates the following quantities:
 Quantity   
 Type   
 Description  
zuwall.bias
scalar
the instantaneous value of the bias potential
zuwall.force2
scalar
the instantaneous value of the squared force due to this bias potential: UPPER_WALLSDefines a wall for the value of one or more collective variables, More details ARGthe arguments on which the bias is acting=z ATthe positions of the wall=12.0 KAPPAthe force constant for the wall=100 EXP the powers for the walls=2

# activate metadynamics 3D gaussian using 3 colvars:
metadThe METAD action with label metad calculates the following quantities:
 Quantity   
 Type   
 Description  
metad.bias
scalar
the instantaneous value of the bias potential: METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=z,r,theta ...
PACEthe frequency for hill addition=500 HEIGHTthe heights of the Gaussian hills=1.0 # Deposit a Gaussian every 500 time steps (eq to 2ps), with initial height equal to 1.0kJoule/mol
BIASFACTORuse well tempered metadynamics and use this bias factor=15.0 # Bias factor used for well-tempered MetaD ## Lower the biasf the greater hillheights reduction - use higher value for faster sampling; lower value for better convergence
SIGMAthe widths of the Gaussian hills=0.5,0.5,0.1 # Specify gaussian widths for each colvar (based on fluctuations during unbiased runs)
FILE a file in which the list of added hills is stored=HILLS # Gaussians will be written to file
GRID_MINthe lower bounds for the grid=-18,-1.9,-pi GRID_MAXthe upper bounds for the grid=18,24,pi GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.2,0.2,0.04 # Gaussians will be stored on grid with respective min/max/binsizes for each colvar
TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310 # Temperature of system (required for well-tempered MetaD)
WALKERS_Nnumber of walkers=9 WALKERS_IDwalker id=3 WALKERS_DIRshared directory with the hills files from all the walkers=. WALKERS_RSTRIDEstride for reading hills files=250 # Switch on Multiple Walkers MetaD with a total of 9 possible walkers, starting from walker#0; HILLS files read every 50steps=.2ps, written to DIR WHERE JOB WAS SUBMITTED
# CALC_RCT RCT_USTRIDE=250 # Compute the reweighting factor and rbias every 250 timesteps using for histogram analysis --requires hills to be stored on GRID
...


# Print values of the colvars and all bias potentials on separate COLVAR files for each walker
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=z,r,theta,*.bias FILEthe name of the file on which to output these quantities=COLVAR.3 STRIDE the frequency with which the quantities of interest should be output=250