[gmx-users] Pulling two groups in opposite direction

[Naba]

On Thu, May 17, 2018 at 11:09 AM, Naba <nabajyoti.goswami at gmail.com> wrote:

> On 5/16/18 3:32 AM, Naba wrote:
>> > Dear all,
>> >
>> > I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
>> > acids from its homodimer in opposite directions along z axis. The
>> > interfaces of each protein chain is parallel to the z axis. I do not
>> need
>> > any restraints in this case. I have gone through the GROMACS manual and
>> > some of the previous archived messages and set the following mdp
>> options.
>> >
>> > ; Pull code
>> > pull                    = yes
>> > pull_ngroups            = 2
>> > pull_ncoords            = 2
>> > pull_group1_name        = chain_A
>> > pull_group2_name        = chain_B
>> > ;pull_group3_name = Protein
>> > pull_coord1_type = umbrella
>> > pull_coord2_type = umbrella
>> > pull_coord1_init = 0.0
>> > pull_coord2_init = 0.0
>> > pull_coord1_start = yes           ; define initial COM distance > 0
>> > pull_coord2_start = yes
>> > pull_coord1_geometry    = direction
>> > pull_coord2_geometry    = direction
>> > pull_coord1_groups      = 2 1
>> > pull_coord2_groups      = 1 2
>> > pull_coord1_dim         = N N Y
>> > pull_coord2_dim         = N N Y
>>
>> Note that pull_coord*_dim is not relevant when using "direction" geometry.
>>
>> > pull_coord1_rate        = 0.01        ; 0.008 nm per ps = 8 nm per ns
>> > pull_coord2_rate        = 0.01         ; 0.008 nm per ps = 8 nm per ns
>> > pull_coord1_k           = 2000          ; kJ mol^-1 nm^-2
>> > pull_coord2_k           = 2000
>> > pull_coord1_vec        = 0.0 0.0 1.0
>> > pull_coord2_vec        = 0.0 0.0 -1.0
>> > nstcalcenergy = 1
>> > nhchainlength = 1
>> >
>> > But it fails to pull chain_A in positive z direction. However, chain_B
>> is
>> > seemed to pull in negative z direction. Someone please suggest the
>> proper
>> > way to pull two groups in opposite directions, or if there is anything
>> that
>> > I am missing.
>>
>> What is the point of pulling in two directions? Separation of two
>> species requires only one reaction coordinate. For every action, there
>> is an equal, but opposite reaction...
>>
>> -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
>>
>> ==================================================
>
>
> Thank you Dr. Justin.
Besides PMF calculations during umbrella sampling, I want to observe the
interacting residues while pulling both the chain in opposite directions.
In your tutorial you pulled only one chain for your specific case. Whereas
in my case, the point to be observed how smoothly or rigorously the chains
are interacting with their residues in interface due to the application of
two equal forces in opposite directions.

Anyways, from your reply should I understand that pulling only one chain
without any restraints in only one direction will do my job? Please correct
me the mdp settings.


Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India