[gmx-users] umbrella sampling for two polymer interaction

[gromacs query]

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
>
> *Gesendet:* Donnerstag, 30. Mai 2013 um 14:44 Uhr
> *Von:* "gromacs query" <gromacsquery at gmail.com>
> *An:* "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> *Betreff:* [gmx-users] umbrella sampling for two polymer interaction
> Dear All,
>
> 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
>
> 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?
>
> 3) And also what should be pull_ngroups because if there is no
> reference group then it should be 2
>
> 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
>
> 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)
>
>
> thanks,
>
> Jiom
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