Re: SMD with colvar not working

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Tue Apr 24 2018 - 11:12:17 CDT

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
>>>>>> }
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>

This archive was generated by hypermail 2.1.6 : Fri Oct 18 2019 - 23:19:32 CDT