Re: SMD with colvar not working

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Apr 24 2018 - 10:56:46 CDT

To put it as a question: the distance of interest here is the distance
between the helix and what?

On 24 April 2018 at 17:45, Dhiraj Srivastava <dhirajks_at_gmail.com> wrote:

> 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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