From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Feb 23 2017 - 14:44:00 CST
Hi Brian, you have defined the keywords lower/upper walls, which will
confine the variables by half-harmonic potentials, but not the boundaries
of the PMF grid (lowerBoundary / upperBoundary).
Giacomo
On Thu, Feb 23, 2017 at 3:35 PM, Bennion, Brian <bennion1_at_llnl.gov> wrote:
> Hello,
>
>
>
> I have just recompiled namd2.12 with the cvs nightly from Feb 23.
>
> There have been a number of deprecations that I fixed in my colvar input
> file. However, one error remains that I have not figure out yet.
>
> Below is my current colvar file. I just wat to map the potential energy
> surface for two dihedrals of an amino acid in a protein, Chi1 and Chi2.
>
>
>
> The error is:
>
> colvars: Collective variables initialized, 2 in total.
>
> colvars: ------------------------------------------------------------
> ----------
>
> colvars: Initializing a new "metadynamics" instance.
>
> colvars: # name = "metadynamics1" [default]
>
> colvars: # colvars = { chi1, chi2 }
>
> colvars: # outputEnergy = off [default]
>
> colvars: # hillWeight = 0.5
>
> colvars: # newHillFrequency = 3000
>
> colvars: # hillWidth = 2
>
> colvars: Half-widths of the Gaussian hills (sigma's):
>
> colvars: chi1: 10
>
> colvars: chi2: 10
>
> colvars: # multipleReplicas = off [default]
>
> colvars: # useGrids = on [default]
>
> colvars: # gridsUpdateFrequency = 3000 [default]
>
> colvars: # rebinGrids = off [default]
>
> colvars: Feature unavailable: "lower boundary" in colvar chi1
>
> colvars: ...required by "grid" in colvar chi1
>
> colvars: Error: Failed dependency in colvar chi1.
>
> FATAL ERROR: Error in the collective variables module: exiting.
>
> colvarsTrajFrequency 500
>
> colvarsRestartFrequency 500
>
>
>
>
>
> colvar {
>
> name chi1
>
> width 10.0
>
> lowerWall -180
>
> upperWall 180
>
> lowerWallConstant 0.2
>
> upperWallConstant 0.2
>
> outputAppliedForce on
>
> dihedral {
>
> oneSiteSystemForce
>
> group1 {
>
> atomnumbers 3487
>
> }
>
> group2 {
>
> atomnumbers 3489
>
> }
>
> group3 {
>
> atomnumbers 3491
>
> }
>
> group4 {
>
> atomnumbers 3494
>
> }
>
> }
>
> }
>
>
>
> colvar {
>
> name chi2
>
> width 10.0
>
> lowerWall -180
>
> upperWall 180
>
> lowerWallConstant 0.2
>
> upperWallConstant 0.2
>
> outputAppliedForce on
>
> dihedral {
>
> oneSiteTotalForce
>
> group1 {
>
> atomnumbers 3489
>
> }
>
> group2 {
>
> atomnumbers 3491
>
> }
>
> group3 {
>
> atomnumbers 3494
>
> }
>
> group4 {
>
> atomnumbers 3495
>
> }
>
> }
>
> }
>
>
>
> metadynamics {
>
> colvars chi1 chi2
>
> hillWeight 0.5
>
> hillWidth 2
>
> newHillFrequency 3000
>
> }
>
>
>
> *From:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *On
> Behalf Of *Bennion, Brian
> *Sent:* Thursday, February 23, 2017 8:39 AM
> *To:* Giacomo Fiorin <giacomo.fiorin_at_gmail.com>; NAMD list <
> namd-l_at_ks.uiuc.edu>; Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
>
> *Subject:* Re: namd-l: colvars: Error: Feature unavailable:compute total
> collective force only from one group center
>
>
>
> Thank you both for the info.
>
> I am using the NAMD_CVS-2016-11-11_Source for my build. I will compile a
> later version.
>
>
>
> Brian
>
>
> ------------------------------
>
> *From:* Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> *Sent:* Thursday, February 23, 2017 1:10:20 AM
> *To:* NAMD list; Ajasja Ljubetič
> *Cc:* Bennion, Brian
> *Subject:* Re: namd-l: colvars: Error: Feature unavailable:compute total
> collective force only from one group center
>
>
>
> Ajasja pointed correctly to the fix for that bug.
>
> More to that, I believe that the fix is already included in NAMD 2.12: can
> you try it?
>
> Giacomo
>
>
>
> On Thu, Feb 23, 2017 at 2:36 AM, Ajasja Ljubetič <
> ajasja.ljubetic_at_gmail.com> wrote:
>
> Hi!
>
> I'm not 100% sure this is related to your problem, but this was on of the
> larger changes to the colvars module:
> https://colvars.github.io/totalforce.html
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__colvars.github.io_totalforce.html&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=Nc4rBAmwF0p9LnBBNhMpRiAXvXqyIA8RNz8Kk2kCn90&s=yCbl4Q5dCuBZ-92PFxhp0iPz2bkq8Tf61uqyleuQKmw&e=>
>
> Also, there is one hit with this error here:
> https://github.com/colvars/colvars/issues/89
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_colvars_colvars_issues_89&d=DwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6cQ04kjNHUuxT8SDe1wb0TtPDsnWRp4T4iwoYRLFpsY&m=Nc4rBAmwF0p9LnBBNhMpRiAXvXqyIA8RNz8Kk2kCn90&s=X4Iku8BTWbq1vhFT_wKafCW2luDahtDtzy8ZY1rChpk&e=>
>
>
>
> Best,
>
> Ajasja
>
>
>
> On 23 February 2017 at 01:17, Bennion, Brian <bennion1_at_llnl.gov> wrote:
>
> Hello,
>
> Getting back to some work I did last year with metadynamics. Hardware has
> been updated since then as well as the version of namd.
>
> I have scanned the email list for the error described below but have not
> found anything yet. I know that there has been a fair amount of work in
> the colvars modules in between namd.10 and namd2.12. Perhaps I just need
> to alter a keyword. The colvar output is below:
>
>
>
> colvars: ------------------------------------------------------------
> ----------
>
> colvars: Initializing the collective variables module, version 2016-10-21--001a114c8222a94339054938ae0a--
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:07 CST