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

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Mon Aug 19 2019 - 13:37:46 CDT

Hi Lucas,

This looks similar to what I've done when I want to have 2 biases going at once (see below), so I don't see why 4 should be a problem. What is in your .traj file? The last four columns should be telling you where the center is *supposed* to be, since you turned output_center on. It may be that you have left wrapping on, so the distance is behaving nicely but is moving your solute to the dummy position through aqueous solution instead of through the channel like you intended. To fix this, take a look at the "forceNoPBC" option for each colvar, and turn off wrapping within NAMD.

-Josh

harmonic {
        name reus
        colvars proteincontact cellcontacts
        centers 0 0
        forceConstant 0.002256 0.002136
        outputCenters on
}

On 2019-08-19 11:51:55-06:00 owner-namd-l_at_ks.uiuc.edu 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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