[gmx-users] Re: umbrella sampling for two polymer interaction

gromacs query gromacsquery at gmail.com
Sat Jun 1 12:01:52 CEST 2013 

Dear Thomas,
>> In AMBER I remember I did once methane-methane interaction, just
distance based umbrella sampling. But there I did not
>>  provide any direction. So should it not be N N N in Gromacs if I want
to allow them freely move in xyz.

Sorry am wrong that should be Y Y Y in Gromcacs! for such case

regards,


On Fri, May 31, 2013 at 10:03 PM, gromacs query <gromacsquery at gmail.com>wrote:

> Dear Thomas,
>
> Thanks a lot again for great reply. Please clarify this also,
>
> >> If one uses only 'Y N N' B would only move along the x-axis due to the
> pull, but could move freely in the yz-plane
> >>You never want to use the pull-code and 'pull_dim = N N N'
> >>This would mean that there is no force acting between your two groups.
> Then one could have skipped using the pull-code...
>
> So keeping Y N N will allow free movement in yz plane. So if I want A B to
> move freely in xyz but just keep them separated by some distance with
> spring const (just like two balloons tied to each other flying in air).
> Sorry confused. In AMBER I remember I did once methane-methane
> interaction, just distance based umbrella sampling. But there I did not
> provide any direction. So should it not be N N N in Gromacs if I want to
> allow them freely move in xyz.
>
> thanks,
>
>
>
> On Fri, May 31, 2013 at 8:53 PM, Thomas Schlesier <schlesi at uni-mainz.de>wrote:
>
>> For comments to your questions see below.
>>
>> More general: (somewhat longer than i wanted. Hope you find some answers
>> here)
>>
>> Imagine two interacting particles A and B which are alinged to the
>> x-axis. We take A as the reference group, B as pulled group and put the
>> origin of the umbrella potential on top of B (pull_start=yes).
>> Simulation starts -> A and B moves.
>> Pull-code step: From A we calculate the new position of the umbrella
>> potential, this is unequal to B, since B moved and our reference point move.
>> Now we have a force acting on B, 'pull_dim' controls in which directions
>> the force acts. With 'Y Y Y' B is pulled towards the origin of the umbrella
>> potential (and with this to the position it should have relative to A).
>> If one uses only 'Y N N' B would only move along the x-axis due to the
>> pull, but could move freely in the yz-plane. In the end one would get a
>> structure where A and B have the right distance in the x-axis but are miles
>> away from each other in the yz-plane.
>>
>> Now imagine we pull B away from A. Since MD simulations normally separete
>> the movement of the center of mass of the system, it would look like A and
>> B would move away from a middle point.
>>
>> (Interchanging A and B should give the same results).
>>
>>
>> Think in your case (doing umbrella sampling) the mdp-file you suggested
>> would be most appropiate (with 'pull_start=yes' and 'pull_ngroups=1'). This
>> gives you a potential which fixes the distance between the two proteins.
>> One thing you should be aware is that if you restrain the distance in 3d,
>> you have to account for entropic effects (see also the GROMACS manual). If
>> you restrain the system only in one direction, these don't arise. Think
>> this is the reason why one sees some work with umbrella sampling were the
>> restraint works only in one direction.
>>
>>
>> Am 31.05.2013 17:20, schrieb gmx-users-request at gromacs.org:
>>
>>  Dear Thomas,
>>>
>>> Thanks a lot for your time and nice explanation. I was not able to get
>>> specially the pull_start flag but now its quite clear.
>>>
>>> I feel sorry, that should be pull_dim = N N N in my case. Also I will be
>>> much thankful if you please can help me to make understand following:
>>>
>>
>> STOP!!!
>> You never want to use the pull-code and 'pull_dim = N N N'
>> This would mean that there is no force acting between your two groups.
>> Then one could have skipped using the pull-code...
>>
>>
>>
>>> 1)
>>>
>>>> >>If you do a pulling simulation, there can be reason for chosing the
>>>>>
>>>> groups (protein = reference , ligand = pulled group, since we want to
>>> pull
>>> it away)
>>>
>>> This indeed is correct but I am not able to get depth of this. I mean to
>>> say lets keep ligand as a reference and protein as pulled group then yes
>>> it
>>> sounds stupid but I am not able to provide a reason myself why we can not
>>> keep ligand as reference and pull protein rather !!
>>>
>>
>> Think this setup should also work. For some simple systems i imagine it
>> should give identical results.
>> For complex system i would also think so. But i can't comment on this
>> with actual expirience. The dimer systems which i investigated were
>> symmetric...
>>
>>
>>
>>
>>>
>>> 2)
>>>
>>>  > >3) And also what should be pull_ngroups because if there is no
>>>>>
>>>>>> >> >reference group then it should be 2
>>>>>>
>>>>> >>
>>>>>
>>>> >Better use a reference group -> pull_ngroups = 1
>>>>
>>> You don't want to pull in absolute coordinates, when your system can
>>> rotate..
>>>
>>> I am not able to understand this part. Can you please provide some
>>> example
>>> so that it makes easier to understand this
>>>
>>
>> Imagine only a single protein which you want to unfold. In an equilibrium
>> simulation the protein can freely rotate in the box. If we use the
>> N-terminus as the reference group and the C-terminus a the pulled group,
>> the origin of the umbrella potential will always be updated and will
>> account for movement of the N-terminus (reference group).
>> If one would pull in absolute coordinates, one would need to give the
>> position of the umbrella potential in absolute space. The molecule can
>> move, but the origin of the potential will always stay fixed at one place.
>> Think in the end this would be equal to an position restraint of said group.
>> If one would want to restrain the distance of two groups in such a way,
>> one would need two umbrella potentials. But since these would be equal to
>> two position restraints, there would be no coupling between the two. I
>> mean, if both groups move around but would have the same distance it should
>> be ok since the distance is fine. But both umbrella potential would pull
>> each group back to the initial position.
>>
>>
>>
>>>
>>> Much thanks again,
>>>
>>>
>>> regards,
>>> Jiom
>>>
>>>
>>>
>>>
>>> On Fri, May 31, 2013 at 1:21 PM, Thomas Schlesier<schlesi at uni-mainz.de**
>>> >wrote:
>>>
>>>  >Look also into the manual. But the tutorial is a nice place to start.
>>>> >For further comments see below:
>>>> >
>>>> >
>>>> >  Dear Lloyd,
>>>>
>>>>> >>
>>>>> >>I have read that but my system is different
>>>>> >>
>>>>> >>regards,
>>>>> >>
>>>>> >>
>>>>> >>On Thu, May 30, 2013 at 8:28 PM, lloyd riggs<lloyd.riggs at gmx.ch>
>>>>> wrote:
>>>>> >>
>>>>> >>  >Dear Jiom,
>>>>>
>>>>>> >>> >
>>>>>>> >>> >Look at justines tutorial, there's example pull .mdp.
>>>>>>> >>> >
>>>>>>> >>> >Stephan Watkins
>>>>>>> >>> >
>>>>>>>
>>>>>> >>>
>>>>>>
>>>>> >>
>>>>>
>>>> >  >
>>>>
>>>>> >>>
>>>>>>
>>>>>>> >>> >I want to do Umbrella sampling between two different polymers
>>>>>>> (A and B)
>>>>>>> >>> >interacting with each other with starting configuration
>>>>>>> separated by
>>>>>>>
>>>>>> >>>some
>>>>>>
>>>>>>> >>> >distance and I am trying to bring them closer.
>>>>>>> >>> >
>>>>>>> >>> >I have some queries regarding pull inputs: (this is for to run a
>>>>>>>
>>>>>> >>>umbrella
>>>>>>
>>>>>>> >>> >sampling at some distance)
>>>>>>> >>> >
>>>>>>> >>> >pull = umbrella
>>>>>>> >>> >pull_geometry = distance
>>>>>>> >>> >pull_dim = Y Y Y
>>>>>>> >>> >pull_start = ???
>>>>>>> >>> >pull_ngroups = 2?
>>>>>>> >>> >pull_group0 = polymer_B
>>>>>>> >>> >pull_group1 = polymer_A
>>>>>>> >>> >pull_init1 = 0
>>>>>>> >>> >pull_rate1 = 0.0
>>>>>>> >>> >
>>>>>>> >>> >
>>>>>>> >>> >please suggest for following:
>>>>>>> >>> >
>>>>>>> >>> >1) pull_dim I have set to Y Y Y: Is this correct I do not want
>>>>>>> to make
>>>>>>> >>> >it interact with some directional vector
>>>>>>>
>>>>>> >>>
>>>>>>
>>>>> >>
>>>>>
>>>> >I don't really understand the question. If you use 'pull_dim = Y Y Y'
>>>> the
>>>> >pulling potential acts in all 3 dimensions, if you use 'pull_dim = Y N
>>>> N'
>>>> >the pulling potential acts only in the X direction and your two groups
>>>> an
>>>> >move freely in the YZ-plane.
>>>> >
>>>> >
>>>> >  >
>>>>
>>>>> >>> >2) Which should be group0 or group1, in other words should I pull
>>>>>>> both
>>>>>>> >>> >together or how I should decide which one should be reference
>>>>>>> and
>>>>>>> >>> >which to be pulled as both are different polymers?
>>>>>>>
>>>>>> >>>
>>>>>>
>>>>> >>Depends on what you want to do. Easiest way would be define one
>>>>> polymer a
>>>>>
>>>> >group0/reference group and the other as group1/pulled group. System
>>>> >shouldn't care about which polymer is which group.
>>>> >If you do a pulling simulation, there can be reason for chosing the
>>>> groups
>>>> >(protein = reference , ligand = pulled group, since we want to pull it
>>>> away)
>>>> >
>>>> >
>>>> >  >
>>>>
>>>>> >>> >3) And also what should be pull_ngroups because if there is no
>>>>>>> >>> >reference group then it should be 2
>>>>>>>
>>>>>> >>>
>>>>>>
>>>>> >>Better use a reference group -> pull_ngroups = 1
>>>>>
>>>> >You don't want to pull in absolute coordinates, when your system can
>>>> >rotate...
>>>> >
>>>> >
>>>> >  >
>>>>
>>>>> >>> >4) I am not able to understand pull_start option with pull_init1.
>>>>>>> In
>>>>>>> >>> >this case if it is set to yes and 0.0 respectively then does
>>>>>>> that mean
>>>>>>> >>> >this combination is equivalent to pull_start = No if I just
>>>>>>> assume
>>>>>>> >>> >pull_init1 does not have any default value (which is 0.0); not
>>>>>>> >>> >existing
>>>>>>>
>>>>>> >>>
>>>>>>
>>>>> >> From the setup which you have written above:
>>>>>
>>>> >polymer_B is the reference group. the origin of the pulling potential
>>>> is
>>>> >at 'pull_init1' (a length) along the vector which goes from polymer_B
>>>> to
>>>> >polymer_A (sine you use pull_geometry = distance).
>>>> >If you set pull_init1=0 and pull_start=no, polymer_A will crash into
>>>> >polymer_B (since the origin of the umbrella potential is directly at
>>>> the
>>>> >center of mass of polymer_B).
>>>> >If you set pull_init1=0 and pull_start=yes, GROMACS adds the distance
>>>> >between polymer_B and A to pull_init1 (-> so pull_init1 is now greater
>>>> than
>>>> >0.0). Now the origin of the umbrella potential is at the center of
>>>> mass of
>>>> >polymer_A. -> A is restrainted to a certian distance of B.
>>>> >
>>>> >  >
>>>>
>>>>>  >>> >5) Also finally where are upper and lower bounds defined.
>>>>>>> pull_k1 =
>>>>>>> >>> >1000 is harmonic applied to some equilibrium distance value.
>>>>>>> How this
>>>>>>> >>> >distance is taken by the programme (or it is just the starting
>>>>>>> >>> >distance taken between two groups) and what are the ?? values
>>>>>>>
>>>>>> >>>
>>>>>>
>>>>>>> >>> >defined. (say in AMBER I define r1,r2,r3,r4; where r2=r3 which
>>>>>>> is
>>>>>>> >>> >assumed equilibrium value and r1 is lower and r4 is upper value
>>>>>>> which
>>>>>>> >>> >defines shape of potential)
>>>>>>>
>>>>>> >>>
>>>>>>
>>>>> >>The umbrella potential is a simple harmonic potential (so no fancy
>>>>> stuff
>>>>>
>>>> >as in AMBER) with
>>>> >V = 1/2 k x^2
>>>> >where x is the violation of the equilibrium distance.
>>>> >For your setup
>>>> >V = 1/2 (pull_init1 - distance(B-A))^2
>>>> >where distance(B-A) means the distance between both polymers.
>>>> >
>>>> >
>>>> >Greetings
>>>> >Thomas
>>>>
>>>
>> --
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