From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Jul 29 2021 - 08:31:43 CDT
Hello Vidhya, I'm not sure where you have line break characters (which may
have changed when you pasted into the email), but their position will
matter.
I would begin by checking the documentation for what you're using here,
which is the Colvars module. Because Colvars is distributed with NAMD for
your own convenience, you may also check the embedded chapter in the NAMD
user's guide, but I would argue that the one on the Colvars webpage is
easier to navigate:
https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html*sec:colvars_config_syntax__;Iw!!DZ3fjg!riXNzsraGMI_H1QpHtDzXVDWCPWPvP4b-V_0iXhlAAKAJG__IJQzNgJvVWt5mvyGLA$
If you appreciate this distinction, it would make it easier for you to find
the correct information.
I can't say for sure what is the problem there (there are a few issues that
may play into the Colvar parser's weaknesses). Try writing down a simple
CV with just one RMSD function:
https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-namd/colvars-refman-namd.html*sec:cvc_rmsd__;Iw!!DZ3fjg!riXNzsraGMI_H1QpHtDzXVDWCPWPvP4b-V_0iXhlAAKAJG__IJQzNgJvVWsB-1W1tQ$
without scriptedFunction for now. I'm all in favor of using someone else's
input as a starting template, but if you don't check yourself what the
keywords mean in the doc, you won't get very far with advanced methodology
such as enhanced sampling. When you can make it work for one RMSD by
fixing all the typos, it's straightforward to add the other RMSD terms.
It is also tedious to try and start a new NAMD simulation each time, so why
not download the latest VMD alpha build and try the Dashboard GUI?
https://urldefense.com/v3/__https://colvars.github.io/colvars-refman-vmd/colvars-refman-vmd.html*sec:dashboard__;Iw!!DZ3fjg!riXNzsraGMI_H1QpHtDzXVDWCPWPvP4b-V_0iXhlAAKAJG__IJQzNgJvVWuOT71IAA$
On Thu, Jul 29, 2021 at 8:52 AM Vidhya Sankar <
vidhyasankar7928_at_remove_yahoo.com> wrote:
> Dear Namd users i tried form metadybamics us RMSD as CV i have following
> input files
>
>
> colvar {
> name s
>
> width 1
>
> lowerboundary 70
> upperboundary 145
>
> lowerwallconstant 10.0
> upperwallconstant 10.0
>
> scriptedFunction source.tcl
>
> # extendedLagrangian on
> # extendedFluctuation 0.01
>
> rmsd {
> group1
> atomNumbersRange 1-1589
>
> refpositionsfile 0.pdb
> componentExp 1 }
> rmmsd {
> group2
> atomNumbersRange 1-1589
> refpositionsfile 1000.pdb
> componentExp 2 }
> rmsd {
> group3
> atomNumbersRange 1-1589
>
> refpositionsfile 2000.pdb
> componentExp 3 }
> rmsd {
> group4
> atomNumbersRange 1-1589
>
> refpositionsfile 3000.pdb
> componentExp 4 }
> group5
> atomNumbersRange 1-1589
>
> refpositionsfile 4000.pdb
> componentExp 5 }
> rmsd {
> group6
> atomNumbersRange 1-1589
>
> refpositionsfile 5000.pdb
> componentExp 6 }
> rmsd {
> group7
> atomNumbersRange 1-1589
>
> refpositionsfile 6000.pdb
> componentExp 7 }
> rmsd {
> group8
> atomNumbersRange 1-1589
>
> refpositionsfile 7000.pdb
> componentExp 8 }
> rmsd {
> group9
> atomNumbersRange 1-1589
>
> refpositionsfile 8000.pdb
> componentExp 9 }
> rmsd {
> group10
> atomNumbersRange 1-1589
>
> refpositionsfile 9000.pdb
> componentExp 10 }
>
> }
>
> #############################################################
> # ABF section
> #############################################################
>
> abf {
> colvars s
> fullSamples 500
> }
>
>
> *But when i run the meta dynamics i gt the following error*
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *colvars:
> ----------------------------------------------------------------------
> colvars: Reading new configuration: colvars: # smp = on [default] colvars:
> # analysis = off [default] colvars: # colvarsTrajFrequency = 1000 colvars:
> # colvarsRestartFrequency = 10000 [default] colvars: # scriptedColvarForces
> = off [default] colvars: # scriptingAfterBiases = off [default] colvars:
> Warning: no collective variables defined. colvars: Collective variables
> initialized, 0 in total. colvars: No collective variables biases were
> defined. colvars:
> ----------------------------------------------------------------------
> colvars: Collective variables module (re)initialized. colvars:
> ----------------------------------------------------------------------
> colvars:
> ----------------------------------------------------------------------
> colvars: Reading new configuration from file "pathCV1.in": colvars: Error:
> unmatched curly braces in configuration. FATAL ERROR: Error in the
> collective variables module: exiting. ------------- Processor 0 Exiting:
> Called CmiAbort ------------ Reason: FATAL ERROR: Error in the collective
> variables module: exiting. *
>
>
> What are the mistake i did it would be useful if any one of you pointed
> out Even i tried lot i could not trace out error
>
> With regards
> S.VIDHYASNKAR
>
>
>
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