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

From: Lucas Neumann (lucas95n_at_gmail.com)
Date: Wed Aug 21 2019 - 09:18:39 CDT

That was exactly it, thanks!

Em seg, 19 de ago de 2019 às 15:37, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
escreveu:

> 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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