PLUMED-NEST

Project ID: plumID:24.028
Source: inputs/tip3p/U/metadyn/plumed_puckering.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

MOLINFOThis command is used to provide information on the molecules that are present in your system. More details STRUCTUREa file in pdb format containing a reference structure=../conf.pdb MOLTYPE what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible=rna
The MOLINFO action with label  calculates somethingpuck1The PUCKERING action with label puck1 calculates the following quantities:
 Quantity   
 Type   
 Description  
puck1.phs
scalar
Pseudorotation phase (5 membered rings)
puck1.amp
scalar
Pseudorotation amplitude (5 membered rings)
puck1.Zx
scalar
Pseudorotation x Cartesian component (5 membered rings)
puck1.Zy
scalar
Pseudorotation y Cartesian component (5 membered rings): PUCKERINGCalculate sugar pseudorotation coordinates. More details ATOMSthe five or six atoms of the sugar ring in the proper order=@sugar-2the heavy atoms of the sugar in residue 2. Click here for more information. 
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=puck1.Zx,puck1.Zy FILEthe name of the file on which to output these quantities=PUCKERING