Re: Can't set multiple harmonic restrains in colvar module

From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Mon Aug 19 2019 - 15:06:23 CDT

Have you tried splitting the harmonic block into four blocks?


On Mon, Aug 19, 2019 at 1:45 PM Lucas Neumann <lucas95n_at_gmail.com<mailto:lucas95n_at_gmail.com>> wrote:
How can I set multiple colvars with harmonic restrains? I'm trying to push 4 solute molecules through a small channel -- for that, I am setting 4 different colvars with group1 as one of the solute atoms and group2 as a dummy atom in the channel exit. But in the dcd file, it seems that only one harmonic restraining was initialized (only one molecule enters the channel). The colvars initialization in the .log file seems normal, I already tried to use a bigger force constant, but with no results. DO anyone how if is there something wrong with my colvar config file?

Bellow the colvar settings file I'm using:

colvar.inp:

colvarsTrajFrequency 100
colvar {
    name aaa
    distance {
        group1 {
            atomsFile input/gly_a.pdb
            atomsCol O
            atomsColValue 2.0
        }
        group2 {
            dummyAtom (17.803, 16.004, 25.500)
        }
    }
}
colvar {
    name bbb
    distance {
        group1 {
            atomsFile input/gly_b.pdb
            atomsCol O
            atomsColValue 2.0
        }
        group2 {
            dummyAtom (-25.433, 15.428, 25.500)
        }
    }
}
colvar {
    name ccc
    distance {
        group1 {
            atomsFile input/gly_c.pdb
            atomsCol O
            atomsColValue 2.0
        }
        group2 {
            dummyAtom (-2.612, -6.859, 25.500)
        }
    }
}
colvar {
    name ddd
    distance {
        group1 {
            atomsFile input/gly_d.pdb
            atomsCol O
            atomsColValue 2.0
        }
        group2 {
            dummyAtom (-4.268, 36.770, 25.500)
        }
    }
}
harmonic {
  colvars aaa bbb ccc ddd
  forceConstant 20.0 20.0 20.0 20.0
  centers 50.0 50.0 50.0 50.0
  targetCenters 0.0 0.0 0.0 0.0
  targetNumSteps 10000000
  outputCenters on
}


Lucas,

PhD Candidate

Chemistry

Institute of Chemistry

University of Campinas

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