Re: SMD with colvar not working

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Tue Apr 24 2018 - 12:50:47 CDT

You need to look at the colvars trajectory and see the initial value of the
distance. Then pull starting from that value.

On 24 April 2018 at 18:12, Dhiraj Srivastava <dhirajks_at_gmail.com> wrote:

> I did tried it. so in my ref selection, I used rest of the protein but
> immediately after the start of the run the helix is getting pulled in a way
> that does not looks right. what I think the problem is that I am defining
> the centers as 0 but the distance between the entire helix (Calpha atoms)
> and rest of the protein (or any other atom) can not be zero (and can not be
> defined by one number). So is it not possible to apply the pulling force on
> entire helix CA atoms and should I be picking only one atom of the helix?
>
> Thanks
> Dhiraj
>
>
> On Tue, Apr 24, 2018 at 11:04 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
> wrote:
>
>> What I mean is, the distance can be defined between the helix and the
>> part of the protein that surrounds the helix. That should be the reference
>> group.
>>
>> On 24 April 2018 at 18:02, Dhiraj Srivastava <dhirajks_at_gmail.com> wrote:
>>
>>> unfortunately I don't know the end result. our hypothesis is that the
>>> helix got pulled out (and/or rotated) of the protein to perform the
>>> function and we are speculating that it got pulled somewhere along its
>>> axis. we want to explore the different possibility and then test it by
>>> biochemical means later on.
>>> So that's why I am trying to pull it along the helical axis. I am
>>> planning to test the different conformations along the trajectory to see if
>>> it fits our biochemical constrains.
>>>
>>> Thanks
>>> Dhiraj
>>>
>>> On Tue, Apr 24, 2018 at 10:56 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
>>> wrote:
>>>
>>>> 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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