Fwd: Cannot find colvar dih1 (dih colvars)

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Dec 23 2014 - 14:23:04 CST

I forgot to add that from colvars code I had noticed

}
00208
00209 if (!colvars
<http://www.ks.uiuc.edu/Research/namd/doxygen/classcolvarmodule.html#s6>.size())
{
00210 cvm::log
<http://www.ks.uiuc.edu/Research/namd/doxygen/classcolvarmodule.html#e17>
("Warning: no collective variables defined.\n");
00211 }

however could not relate "size" with my colvars.

farncesco pietra

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Tue, Dec 23, 2014 at 6:15 PM
Subject: Cannot find colvar dih1 (dih colvars)
To: NAMD <namd-l_at_ks.uiuc.edu>

Hello:
New to dih colvars (Linux-multicore-64 namd2.10, minimization), I was
unable to have colvars read:

log file:
colvars: Reading new configuration from file "./MOL_dihe_colvars.in":
colvars: # indexFile = "" [default]
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 100 [default]
colvars: # colvarsRestartFrequency = 100 [default]
colvars: # colvarsTrajAppend = off [default]
colvars: Warning: no collective variables defined.
colvars: Collective variables initialized, 0 in total.
colvars:
----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = MOL_dihe_harmonic
colvars: # colvars = { dih1, dih2, dih3, dih4, dih5, dih6, dih6, dih7,
dih8, dih9, dih10, dih11, dih12, colvars, dih13, dih14, dih15, dih16,
dih17, dih18, dih19, dih20, dih21, dih22, dih23, dih24 }
colvars: Error: cannot find a colvar named "dih1".

The .in file reads (atom ID is given):

colvarsTrajFrequency 100 # output values every 100 steps (default)
 colvarsRestartFrequency 200 # must be > colvarsTrajFrequency
 colvar {
  name dih1 # needed to identify the variable
  width 1.0 # twice the standard deviation during
            # very short simulation; default 1.0
  lowerBoundary -180.0 # lowest end of interval colvar value
  upperBoundary 180.0 # defines the highest possible or allowed value
  outputSystemForce yes # reports also the system force on this
                           # colvar in addition to the current value
  dihedral {
    group1 {
      atomNumbers 63 # FE
    }
    group2 {
      atomNumbers 38 # O6
    }
    group3 {
      atomNumbers 36 # C17
    }
    group4 {
      atomNumbers 37 # O5
    }
    }
 colvar {
  name dih2 # needed to identify the variable
  width 1.0 # twice the standard deviation during
            # very short simulation; default 1.0
  lowerBoundary -180.0
  upperBoundary 180.0
  outputSystemForce yes # reports also the system force on this
                           # colvar in addition to the current value
  dihedral {
    group1 {
      atomNumbers 63
    }
    group2 {
      atomNumbers 38
    }
    group3 {
      atomNumbers 36
    }
    group4 {
      atomNumbers 33 # C16
    }
    }
...................................
.......................................
    }
    }
colvar {
  name dih24 # needed to identify the variable
  width 1.0 # twice the standard deviation during
            # very short simulation; default 1.0
  outputSystemForce yes # reports also the system force on this
                           # colvar in addition to the current value
  dihedral {
    group1 {
      atomNumbers 59
    }
    group2 {
      atomNumbers 9 # O2
    }
    group3 {
      atomNumbers 18 # O4
    group4 {
      atomNumbers 4 # C3
     }
   }
 }
harmonic {

name MOL_dihe_harmonic # arbitrary

colvars dih1 dih2 dih3 dih4 dih5 dih6 dih6 dih7 dih8 dih9 dih10 dih11
dih12 colvars dih13 dih14 dih15 dih16 dih17 dih18 dih19 dih20 dih21 dih22
dih23 dih24

forceConstant 5.0 # in place of lowerWall upperWall
 }

Thanks for help

francesco pietra

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