Re: SMD with colvar not working

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Apr 24 2018 - 04:27:49 CDT

Hi,

If you inspect the colvars trajectory, you might see something that sets
you on the right path. I suspect your "dist" coordinate is always zero.
What could cause that?

Jerome

On 24 April 2018 at 07:21, Dhiraj Srivastava <dhirajks_at_gmail.com> wrote:

> Hi
> I am trying to pull an alpha helix of my protein using colvar component
> distanceZ. however it seems that its not able to pull it out of my protein.
> the helix is slightly curved and it seems to be able to straighten it up
> during the first picosecond of simulation but after that there it seems to
> stay at its place. below is my script. I have doubt about reference
> position. I am choosing entire helix to apply pulling force. and I am
> choosing entire helix as reference position. is that correct way of doing
> SMD with distanceZ colvar. my final goal is to apply rotation and pulling
> force at the same time. rotation is working.
>
> thanks
> Dhiraj
>
> colvar {
> name dist
> outputAppliedForce on
> width 0.1
> lowerBoundary 0.0
> upperBoundary 30
> hardLowerBoundary yes
> hardUpperBoundary yes
>
> distanceZ {
> main {
> psfSegID AP1
> atomNameResidueRange CA 211-235
> }
> ref {
> psfSegID AP1
> atomNameResidueRange CA 211-235
> }
> axis { (-0.22284841537475586, 0.4576619863510132, 0.8607462048530579)}
> forceNoPBC no
> oneSiteSystemForce no
> }
> }
>
> harmonic {
> name steery
> colvars dist
> forceConstant 1
> centers 0
> targetCenters -30
> targetNumSteps 100000
> outputCenters yes
> outputAccumulatedWork yes
> }
>
>

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