Re: SMD with colvar not working

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Tue Apr 24 2018 - 10:45:24 CDT

yes. its not moving. I am suspecting that my reference is not right. but
then what should be the reference? a dummy atom that I should put at the
geometric centre of the helix?

Thanks
Dhiraj

On Tue, Apr 24, 2018 at 4:27 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:

> 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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