[gmx-users] pulling in opposite direction
Justin Lemkul
jalemkul at vt.edu
Wed Oct 10 02:23:50 CEST 2018
On 10/8/18 3:22 AM, Rakesh Mishra wrote:
> Dear Dr. Justin
>
> Thanks for your patience to reply me. I think for last 3-4 months
> we are discussing about the pulling. I agreed with your statement to
> [stop thinking concretely in terms of a "reference" and a
> "pulled" group ]. I am also not thinking in terms of this nomenclature.
> I just thought as a end coordinate of bias. I checked many combination
> for pulling two groups in opposite direction. Now I am getting fine to
> pull groups
> by applying two bias potential. like..
>
> ; Pull code
> pull = yes
> pull_ngroups = 4
> pull_ncoords = 2
> pull_group1_name = r_24
> pull_group2_name = r_12
> pull_group3_name = r_24
> pull_group4_name = r_12
> ; definition of reaction coordinate 1, group 1-2
> pull_coord1_type = umbrella ; harmonic biasing force
> pull_coord1_geometry = distance ; simple distance increase
> pull_coord1_groups = 1 2
> pull_coord1_dim = Y N N
> pull_coord1_rate = 0.005 ; 0.005 nm per ps = 5nm per 1 ns
> pull_coord1_k = 500 ; kJ mol^-1 nm^-2
> pull_coord1_start = yes ; define initial COM distance >
> 0
> ; definition of reaction coordinate 2, group 3-4
> pull_coord2_type = umbrella ; harmonic biasing force
> pull_coord2_geometry = distance ; simple distance increase
> pull_coord2_groups = 3 4
> pull_coord2_dim = Y N N
> pull_coord2_rate = 0.005 ; 0.005 nm per ps = 5nm per 1
> ns
> pull_coord2_k = 500 ; kJ mol^-1 nm^-2
> pull_coord2_start = yes ; define initial COM distance
>> 0
> In this way I am getting conceptually correct output. Now there is no
> changes
> of out put value of force-time by changing the saving frequency of
> co-ordinates of
> position , energy etc, which I was getting previously.
>
> now my request is that please check above pull protocol. lastly in this
> discussion
> I have two query.
> 1- Reaction coordinate means what ? . In my view its position coordinate.
Google is your friend.
> i.e end to
> end distance between two groups during pulling or something else.
>
> 2- Here in above protocol,
> pull_coord1_dim = Y N N
> pull_coord1_dim = Y N N
> this is showing that groups are pulling in x direction and not in Y
> and Z direction.
>
> so what will be the need to define
> pull_coord1_vec = 1 0 0
> pull_coord2_vec = 1 0 0 .
The different geometry specifications have different requirements. The
"distance" method requires Y/N, whereas the "direction" method requires
a vector.
-Justin
> I think both are presenting the same thing.
> Hoping your previous views on my these query. I think after that I will
> have almost
> negligible doubts regarding pulling.
>
> And one another thing is that, If we want to change the pulling protocol
> like to apply
> force as piconewton/ps then in algorithm of gromacs, where we need to
> implement in installed
> gromacs in our machine.
>
>
>
>
>
>
> On Fri, Oct 5, 2018 at 7:10 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 10/5/18 12:47 AM, Rakesh Mishra wrote:
>>> Dear Justin thanks for ur reply.
>>> Which means in this case,both group will act as a reference group for
>> each
>>> other.
>>>
>>> Then now my question is, why without using two biasing potential, in case
>>> of using one
>>> biasing potential for two group, If I do not constrained reference group
>>> then it automatically
>>> move in the opposite direction w.r.t pulling group.
>> I feel like I've already explained how all of this works. The bias is
>> applied to the specified groups, and they evolve however they're going
>> to under the influence of the applied force.
>>
>> It may help to stop thinking concretely in terms of a "reference" and a
>> "pulled" group. That's a conceptual convention that is actually somewhat
>> outdated now that GROMACS supports multiple, simultaneous biasing
>> potentials. Each group defines the end of a reaction coordinate. Their
>> relative positions matter in terms of defining the direction of the
>> bias, hence the "reference" and "pulled" nomenclature. But again, I
>> think that by enforcing such nomenclature, it's a bit misleading.
>>
>> -Justin
>>
>>> On Thu, Oct 4, 2018 at 6:48 PM Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>> On 10/4/18 3:09 AM, Rakesh Mishra wrote:
>>>>> Dear all.
>>>>>
>>>>> How it is possible to pull reference group as well as pull group using
>>>>> gromacs protocol simultaneously in opposite direction using umbrella
>>>>> protocol
>>>>> of pulling. So far non of the Gromacs expertise have given the answer
>> of
>>>>> this question. Hoping from response
>>>>>
>>>> If you want to pull two things in opposite directions, you need two
>>>> biasing potentials.
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Virginia Tech Department of Biochemistry
>>>>
>>>> 303 Engel Hall
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.thelemkullab.com
>>>>
>>>> ==================================================
>>>>
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>>> posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>> * For (un)subscribe requests visit
>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>
>
--
==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com
==================================================
More information about the gromacs.org_gmx-users
mailing list