PLUMED-NEST by plumed-nest

Project ID: plumID:22.033
Source: plumed.dat
Originally used with PLUMED version: 2.7
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
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A TIMEthe units of time=ps ENERGYthe units of energy=kcal/mol
The UNITS action with label  calculates somethingCOMCalculate the center of mass for a group of atoms. More details ATOMSthe list of atoms which are involved the virtual atom's definition=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,17,18,20,21,22,23,24,25,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69 LABELa label for the action so that its output can be referenced in the input to other actions=COM_ligThe COM action with label COM_lig calculates the following quantities: Quantity    Type    Description  
COM_lig 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=168,209,302,343,436,477,570,611,704,745,838,879,972,1013,1106,1147,1240,1281,1374,1415,1508,1549,1642,1683,1776,1817,1910,1951,2044,2085,2178,2219,2312,2353,2446,2487,2580,2621,2714,2755,2848,2889,2982,3023,3116,3157,3250,3291,3384,3425,3518,3559,3652,3693,3786,3827,3920,3961,4054,4095,4188,4229,4322,4363,4456,4497,4590,4631,4724,4765,4858,4899,4992,5033,5126,5167,5260,5301,5394,5435,5528,5569,5662,5703,5796,5837,5930,5971,6064,6105,6198,6239,6332,6373,6466,6507,6600,6641,6734,6775,6868,6909,7002,7043,7136,7177,7270,7311,7404,7445,7538,7579,7672,7713,7806,7847,7940,7981,8074,8115,8208,8249,8342,8383,8476,8517,8610,8651,8744,8785,8878,8919,9012,9053,9146,9187,9280,9321,9414,9455,9548,9589,9682,9723,9816,9857,9950,9991 PHASES Compute center using trigonometric phases LABELa label for the action so that its output can be referenced in the input to other actions=COM_memThe COM action with label COM_mem calculates the following quantities: Quantity    Type    Description  
COM_mem atoms virtual atom calculated by COM action
DISTANCECalculate the distance/s between pairs of atoms. More details ATOMSthe pair of atom that we are calculating the distance between=COM_mem,COM_lig SCALED_COMPONENTS calculate the a, b and c scaled components of the distance separately and store them as label LABELa label for the action so that its output can be referenced in the input to other actions=COM_lig_distThe DISTANCE action with label COM_lig_dist calculates the following quantities: Quantity    Type    Description  
COM_lig_dist.a scalar the normalized projection on the first lattice vector of the vector connecting the two atoms
COM_lig_dist.b scalar the normalized projection on the second lattice vector of the vector connecting the two atoms
COM_lig_dist.c scalar the normalized projection on the third lattice vector of the vector connecting the two atoms
DRRUsed to performed extended-system adaptive biasing force(eABF) This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=COM_lig_dist.c FULLSAMPLES number of samples in a bin prior to application of the ABF=200000 GRID_MINthe lower bounds for the grid (GRID_BIN or GRID_SPACING should be specified)=-0.5 GRID_MAXthe upper bounds for the grid (GRID_BIN or GRID_SPACING should be specified)=0 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.001 TEMPthe system temperature - needed when FRICTION is present=310 FRICTION add a friction to the variable, similar to extended Langevin Damping in Colvars=8.0 TAU specifies relaxation time on each of variables are, similar to extended Time Constant in Colvars=0.5 TEXTOUTPUT use text output for grad and count files instead of boost::serialization binary output OUTPUTFREQwrite results to a file every N steps=2500000 HISTORYFREQsave history to a file every N steps=25000000 DRR_RFILEspecifies the restart file (=drr_lo LABELa label for the action so that its output can be referenced in the input to other actions=drr_loThe DRR action with label drr_lo calculates the following quantities: Quantity    Type    Description  
drr_lo.bias scalar the instantaneous value of the bias potential
drr_lo.COM_lig_dist.c_fict scalar one or multiple instances of this quantity can be referenced elsewhere in the input file. These quantities will named with the arguments of the bias followed by the character string _tilde. It is possible to add forces on these variable. This particular component measures this quantity for the input CV named COM_lig_dist.c
drr_lo.COM_lig_dist.c_vfict scalar one or multiple instances of this quantity can be referenced elsewhere in the input file. These quantities will named with the arguments of the bias followed by the character string _tilde. It is NOT possible to add forces on these variable. This particular component measures this quantity for the input CV named COM_lig_dist.c
drr_lo.COM_lig_dist.c_biasforce scalar The bias force from eABF/DRR of the fictitious particle. This particular component measures this quantity for the input CV named COM_lig_dist.c
drr_lo.COM_lig_dist.c_springforce scalar Spring force between real CVs and extended CVs This particular component measures this quantity for the input CV named COM_lig_dist.c
drr_lo.COM_lig_dist.c_fictNoPBC scalar the positions of fictitious particles (without PBC). This particular component measures this quantity for the input CV named COM_lig_dist.c
DRRUsed to performed extended-system adaptive biasing force(eABF) This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=COM_lig_dist.c FULLSAMPLES number of samples in a bin prior to application of the ABF=200000 GRID_MINthe lower bounds for the grid (GRID_BIN or GRID_SPACING should be specified)=-0.5 GRID_MAXthe upper bounds for the grid (GRID_BIN or GRID_SPACING should be specified)=0 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.001 TEMPthe system temperature - needed when FRICTION is present=310 FRICTION add a friction to the variable, similar to extended Langevin Damping in Colvars=8.0 TAU specifies relaxation time on each of variables are, similar to extended Time Constant in Colvars=0.5 TEXTOUTPUT use text output for grad and count files instead of boost::serialization binary output OUTPUTFREQwrite results to a file every N steps=2500000 HISTORYFREQsave history to a file every N steps=25000000 DRR_RFILEspecifies the restart file (=drr_lo LABELa label for the action so that its output can be referenced in the input to other actions=drr_lo  REFLECTINGWALL whether add reflecting walls for each CV at GRID_MIN and GRID_MAX=0 MAXFACTOR maximum scaling factor of biasing force=1.0
DRRUsed to performed extended-system adaptive biasing force(eABF) This action has hidden defaults. More details ARGthe labels of the scalars on which the bias will act=COM_lig_dist.c FULLSAMPLES number of samples in a bin prior to application of the ABF=200000 GRID_MINthe lower bounds for the grid (GRID_BIN or GRID_SPACING should be specified)=0 GRID_MAXthe upper bounds for the grid (GRID_BIN or GRID_SPACING should be specified)=+0.5 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.001 TEMPthe system temperature - needed when FRICTION is present=310 FRICTION add a friction to the variable, similar to extended Langevin Damping in Colvars=8.0 TAU specifies relaxation time on each of variables are, similar to extended Time Constant in Colvars=0.5 TEXTOUTPUT use text output for grad and count files instead of boost::serialization binary output OUTPUTFREQwrite results to a file every N steps=2500000 HISTORYFREQsave history to a file every N steps=25000000 LABELa label for the action so that its output can be referenced in the input to other actions=drr_upThe DRR action with label drr_up calculates the following quantities: Quantity    Type    Description  
drr_up.bias scalar the instantaneous value of the bias potential
drr_up.COM_lig_dist.c_fict scalar one or multiple instances of this quantity can be referenced elsewhere in the input file. These quantities will named with the arguments of the bias followed by the character string _tilde. It is possible to add forces on these variable. This particular component measures this quantity for the input CV named COM_lig_dist.c
drr_up.COM_lig_dist.c_vfict scalar one or multiple instances of this quantity can be referenced elsewhere in the input file. These quantities will named with the arguments of the bias followed by the character string _tilde. It is NOT possible to add forces on these variable. This particular component measures this quantity for the input CV named COM_lig_dist.c
drr_up.COM_lig_dist.c_biasforce scalar The bias force from eABF/DRR of the fictitious particle. This particular component measures this quantity for the input CV named COM_lig_dist.c
drr_up.COM_lig_dist.c_springforce scalar Spring force between real CVs and extended CVs This particular component measures this quantity for the input CV named COM_lig_dist.c
drr_up.COM_lig_dist.c_fictNoPBC scalar the positions of fictitious particles (without PBC). This particular component measures this quantity for the input CV named COM_lig_dist.c
DRRUsed to performed extended-system adaptive biasing force(eABF) This action uses the defaults shown here. More details ARGthe labels of the scalars on which the bias will act=COM_lig_dist.c FULLSAMPLES number of samples in a bin prior to application of the ABF=200000 GRID_MINthe lower bounds for the grid (GRID_BIN or GRID_SPACING should be specified)=0 GRID_MAXthe upper bounds for the grid (GRID_BIN or GRID_SPACING should be specified)=+0.5 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.001 TEMPthe system temperature - needed when FRICTION is present=310 FRICTION add a friction to the variable, similar to extended Langevin Damping in Colvars=8.0 TAU specifies relaxation time on each of variables are, similar to extended Time Constant in Colvars=0.5 TEXTOUTPUT use text output for grad and count files instead of boost::serialization binary output OUTPUTFREQwrite results to a file every N steps=2500000 HISTORYFREQsave history to a file every N steps=25000000 LABELa label for the action so that its output can be referenced in the input to other actions=drr_up  REFLECTINGWALL whether add reflecting walls for each CV at GRID_MIN and GRID_MAX=0 MAXFACTOR maximum scaling factor of biasing force=1.0
METADUsed to performed metadynamics on one or more collective variables. More details ARGthe labels of the scalars on which the bias will act=drr_lo.COM_lig_dist.c_fict SIGMAthe widths of the Gaussian hills=0.005 HEIGHTthe heights of the Gaussian hills=1.5 PACEthe frequency for hill addition=500 GRID_MINthe lower bounds for the grid=-0.5 GRID_MAXthe upper bounds for the grid=+0.5 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.001 BIASFACTORuse well tempered metadynamics and use this bias factor=8 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310 FILE a file in which the list of added hills is stored=HILLS_lo LABELa label for the action so that its output can be referenced in the input to other actions=metad_loThe METAD action with label metad_lo calculates the following quantities: Quantity    Type    Description  
metad_lo.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=drr_up.COM_lig_dist.c_fict SIGMAthe widths of the Gaussian hills=0.005 HEIGHTthe heights of the Gaussian hills=1.5 PACEthe frequency for hill addition=500 GRID_MINthe lower bounds for the grid=-0.5 GRID_MAXthe upper bounds for the grid=+0.5 GRID_SPACINGthe approximate grid spacing (to be used as an alternative or together with GRID_BIN)=0.001 BIASFACTORuse well tempered metadynamics and use this bias factor=8 TEMPthe system temperature - this is only needed if you are doing well-tempered metadynamics=310 FILE a file in which the list of added hills is stored=HILLS_up LABELa label for the action so that its output can be referenced in the input to other actions=metad_upThe METAD action with label metad_up calculates the following quantities: Quantity    Type    Description  
metad_up.bias scalar the instantaneous value of the bias potential
CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=COM_lig_dist.c FUNCthe function you wish to evaluate=8e-3*step(-x)/(-x) PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=mirror_upThe CUSTOM action with label mirror_up calculates the following quantities: Quantity    Type    Description  
mirror_up scalar an arbitrary function
BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=mirror_up LABELa label for the action so that its output can be referenced in the input to other actions=uw_mirrorThe BIASVALUE action with label uw_mirror calculates the following quantities: Quantity    Type    Description  
uw_mirror.bias scalar the instantaneous value of the bias potential
uw_mirror.mirror_up_bias scalar one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named mirror_up
CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=COM_lig_dist.c FUNCthe function you wish to evaluate=8e-3*step(x)/x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO LABELa label for the action so that its output can be referenced in the input to other actions=mirror_loThe CUSTOM action with label mirror_lo calculates the following quantities: Quantity    Type    Description  
mirror_lo scalar an arbitrary function
BIASVALUETakes the value of one variable and use it as a bias More details ARGthe labels of the scalar/vector arguments whose values will be used as a bias on the system=mirror_lo LABELa label for the action so that its output can be referenced in the input to other actions=lw_mirrorThe BIASVALUE action with label lw_mirror calculates the following quantities: Quantity    Type    Description  
lw_mirror.bias scalar the instantaneous value of the bias potential
lw_mirror.mirror_lo_bias scalar one or multiple instances of this quantity can be referenced elsewhere in the input file. these quantities will named with  the arguments of the bias followed by the character string _bias. These quantities tell the user how much the bias is due to each of the colvars. This particular component measures this quantity for the input CV named mirror_lo
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=* STRIDE the frequency with which the quantities of interest should be output=1000 FILEthe name of the file on which to output these quantities=plumed.log FMTthe format that should be used to output real numbers=%12.4f
FLUSHThis command instructs plumed to flush all the open files with a user specified frequency. More details STRIDEthe frequency with which all the open files should be flushed=1000
Quantity	Type	Description
COM_lig	atoms	virtual atom calculated by COM action
PLUMED-NEST

The public repository of the PLUMED consortium
