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
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:23:09 CST