[gmx-users] Rupture force definition

[Justin Lemkul]

On 1/24/18 5:02 AM, Rakesh Mishra wrote:
> Dear Justin
>
> Thank you very much  for removing the doubts .
> Let me extend  my query in this respect again. As according to pull code
> formate which is  discussed in your testing work of umbrella sampling .
> Please have a rough look.
>
> Pull code
> pull                    = yes
> pull_ngroups            = 2
> pull_ncoords            = 1
> pull_group1_name        = chain_B
> pull_group2_name        = chain_A
> pull_coord1_type        = umbrella      ; harmonic biasing force
> pull_coord1_geometry    = distance      ; simple distance increase
> pull_coord1_groups      =  1 2
> pull_coord1_dim         = Y N N
> pull_coord1_rate        = 0.0005          ; 0.0005 nm per ps = 5 nm per 10
> ns
> pull_coord1_k           = 400          ; kJ mol^-1 nm^-2
> pull_coord1_start       = yes           ; define initial COM distance > 0
>
> As according to some explanation on the net,  I found  that  in the Pull
> code written above,
>
> "pull_group1_name = chain_B "   gromacs read it as a reference group by
> default &
> "pull_group2_name = chain_A"    gromacs read it as a pull group by default.
>
> But suppose, we want to pull 2 or more groups eg.  B2 & B3 in the same
> system and which are having
> two respective reference group A2 & A3 w. r. t. pulled groups  B2 & B3.
> Then how to define these one in above code.
>
> I mean If I have  A1, A2, and A3 three pull group ( which we want to pull)
> and corresponding to these we have three
> reference group B1 , B2 and B3. We are pulling all in the same direction
> (+x  direction ).
> then how to define these simultaneously in above pull code.
>
> will I need to define rate for all these pull group separately ( three
> times) or if rate value is same then no need to
>   define three times corresponding to these three pull groups.

You can define any number of groups to be used in any number of biasing 
potentials. Each needs its own complete definition (geometry, 
dimensions, rate, force constant, etc). Get rid of the notion of 
"reference" and "pull group" in this application; groups define the two 
ends of a reaction coordinate, nothing more.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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