[gmx-users] Re: umbrella sampling for two polymer interaction
gromacsquery at gmail.com
Fri May 31 14:25:50 CEST 2013
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:
>> If you do a pulling simulation, there can be reason for chosing the
groups (protein = reference , ligand = pulled group, since we want to pull
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 !!
> >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
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,
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
>> 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
>>> >distance and I am trying to bring them closer.
>>> >I have some queries regarding pull inputs: (this is for to run a
>>> >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
>>> >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
>> 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.
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