Re: Fwd: Cannot find colvar dih1 (dih colvars)

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Dec 24 2014 - 05:53:54 CST

Thanks to Jeff and Maxim. Yes, there was a "}" less at each colvars.

Still, I have problems with "centers". Setting "0" for each colvars, like
in case of two colvars:

harmonic {
name MOL_dihe_harmonic # arbitrary
colvars dih1 dih2
centers 0 0
forceConstant 5.0 # in place of lowerWall upperWall
 }

is obviously wrong, although accepted in minimization. I was unable to find
how centers should be set in case of multiple dihedral colvars.

thanks for advice

francesco

On Tue, Dec 23, 2014 at 10:59 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:

> I think Jeff is right and after each group4 there should be 3 closing
> brackets, not two.
> Though, I haven’t checked that.
>
> Maxim
>
> > On Dec 23, 2014, at 15:35, Jeff Comer <jeffcomer_at_gmail.com> wrote:
> >
> > Hi Francesco,
> >
> > My guess is that there is a syntax error in the file — a missing "}"
> > or something of the sort. The general way to troubleshoot this is to
> > try to localize the problem. Start with something simple and add more
> > and see when the problem arises. Can you get it to work with just one
> > dihedral? Or just two? Can you whittle down the complexity (for
> > example, by commenting out lines) of the current file until it works?
> > This might help you to find the problem. Another option is to write a
> > script to generate the config file in which you can put safeguards to
> > ensure that you don't have missing braces, etc.
> >
> > Jeff
> >
> > –––––––––––––––––––––––––––––––––––———————
> > Jeffrey Comer, PhD
> > Assistant Professor
> > Institute of Computational Comparative Medicine
> > Nanotechnology Innovation Center of Kansas State
> > Kansas State University
> > Office: P-213 Mosier Hall
> > Phone: 785-532-6311
> >
> >
> > On Tue, Dec 23, 2014 at 3:01 PM, Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
> >> With the .in file containing colvars dih1 and dih2 only, the latter is
> read
> >> correctly. However, dih1 was not found
> >>
> >> Collective variables initialized, 1 in total.
> >> colvars:
> >> ----------------------------------------------------------------------
> >> colvars: Initializing a new "harmonic" instance.
> >> colvars: # name = MOL_dihe_harmonic
> >> colvars: # colvars = { dih1, dih2 }
> >> colvars: Error: cannot find a colvar named "dih1".
> >> colvars: If this error message is unclear, try recompiling with
> >> -DCOLVARS_DEBUG.
> >> FATAL ERROR: Error in the collective variables module: exiting.
> >>
> >> I can not understand what is wrong about the first colvars named "dih1".
> >> Aside from this, where 24 colvars too many?
> >>
> >> thanks for advice
> >>
> >> francesco pietra
> >>
> >>
> >> ---------- Forwarded message ----------
> >> From: Francesco Pietra <chiendarret_at_gmail.com>
> >> Date: Tue, Dec 23, 2014 at 9:23 PM
> >> Subject: Fwd: Cannot find colvar dih1 (dih colvars)
> >> To: NAMD <namd-l_at_ks.uiuc.edu>
> >>
> >>
> >> I forgot to add that from colvars code I had noticed
> >>
> >> }
> >> 00208
> >> 00209 if (!colvars.size()) {
> >> 00210 cvm::log ("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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