[gmx-users] Rupture force definition
jalemkul at vt.edu
Wed Jan 24 13:56:01 CET 2018
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
> 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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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