From: Jiali Wang (jwang204_at_binghamton.edu)
Date: Fri Nov 22 2019 - 19:56:18 CST
Dear Haochuan,
Thank you so much for your help!! Does it means the harmonic constant part,
i also need to make three parts? I found if I list three pair length
together, it's not working?
harmonic {
name lenpot1
colvars length1 length2 length3
forceConstant 1 # in kcal/mol/A^2
centers 4.8 # go from 25 Angstrom RMSD...
outputCenters on
}
Thank you so much for your help!
jiali
On Fri, Nov 22, 2019 at 2:23 PM <yjcoshc_at_gmail.com> wrote:
> Hi Jiali,
>
> You may need four independent colvar sections. For example:
>
> colvar {
>
> name dist1
>
> distance {
>
> ...
>
> }
>
> }
>
> colvar {
>
> name dist2
>
> distance {
>
> ...
>
> }
>
> }
>
> Best regards,
>
> Haochuan Chen
>
>
> 在 2019/11/22 下午12:59, Jiali Wang 写道:
> > Dear NAMD users,
> > Good afternoon, Is that possible to tracking four pair atom distances
> > independently at same time and apply harmonic constant? I am trying to
> > use four part of distance { }. But I found in the colvars.traj file,
> > it only provides one column distance tracking results. Could some help
> > me with this?
> > Thank you for your time!
> > Jiali
> >
> > colvar {
> > name length
> > outputAppliedForce off
> >
> > distance {
> > group1 {
> > atomNumbers 11530
> > }
> > group2 {
> > atomNumbers 10888
> > }
> > }
> > distance {
> > group1 {
> > atomNumbers 5266
> > }
> > group2 {
> > atomNumbers 4624
> > }
> > }
> > distance {
> > group1 {
> > atomNumbers 11794
> > }
> > group2 {
> > atomNumbers 17152
> > }
> > }
> > }
>
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