Project ID: plumID:23.032
Source: ptmtd/plumedpt.dat
Originally used with PLUMED version: 2.9
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
tested onv2.9
tested onmaster
WHOLEMOLECULES
This action is used to rebuild molecules that can become split by the periodic boundary conditions. More details
 
ENTITY0
the atoms that make up a molecule that you wish to align
=1-272

FIT_TO_TEMPLATE
This action is used to align a molecule to a template. More details
 
STRIDE
 the frequency with which molecules are reassembled
=1 
REFERENCE
a file in pdb format containing the reference structure and the atoms involved in the CV
=reference3.pdb 
TYPE
 the manner in which RMSD alignment is performed
=OPTIMAL
ptm: 
PYTORCH_MODEL_CV
This action is not part of PLUMED and was included by using a LOAD command More details
 FILE=plumedpt.pt ATOMS=1,5,13,14,7,10,11,12,15,17,23,24,19,25,27,44,45,29,32,33,42,35,40,37,38,46,48,54,55,50,56,58,71,72,60,63,66,67,68,73,75,95,96,77,80,81,94,83,85,92,86,90,88,97,99,114,115,101,104,106,110,116,118,124,125,120,126,128,136,137,130,133,134,135,138,140,143,144,145,147,150,151,152,162,164,165,159,156,153,166,168,175,176,170,173,177,179,186,187,181,184,188,190,193,194,195,197,217,218,199,202,205,208,210,211,214,219,229,231,232,226,223,220,233,243,245,246,240,237,234,247,257,259,260,254,251,248,261,263,270,271,265,268,272

PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=ptm.node-0,ptm.node-1 
STRIDE
 the frequency with which the quantities of interest should be output
=100 
FILE
the name of the file on which to output these quantities
=COLVAR
metad: 
METAD
Used to performed metadynamics on one or more collective variables. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=ptm.node-0,ptm.node-1 
PACE
the frequency for hill addition
=500 
HEIGHT
the heights of the Gaussian hills
=0.5 
BIASFACTOR
use well tempered metadynamics and use this bias factor
=8 
SIGMA
the widths of the Gaussian hills
=1,1 
FILE
 a file in which the list of added hills is stored
=HILLS
#
# XXX: add something which uses ptm derivatives (METAD, DUMPDERIVATIVES, ...)
# XXX: otherwise Plumed does not allocate memory and PYTORCH_MODEL_CV breaks 
#
# DUMPDERIVATIVES ARG=ptm.* STRIDE=100 FILE=DERIVATIVES FMT=%15.4f