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

[gromacs query]

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:

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 !!


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


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 ą 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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