[gmx-users] Pulling two groups in opposite direction
jalemkul at vt.edu
Thu May 17 14:12:55 CEST 2018
On 5/17/18 1:39 AM, Naba 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
>>> 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 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
> 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.
Do not pull along only one dimension. A normal, soluble protein complex
will rotate in space so you should pull in all three dimensions. There
are several ways to accomplish this pulling, but indeed you only need
one reaction coordinate to induce separation.
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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