[gmx-users] umbrella sampling for two polymer interaction

gromacs query gromacsquery at gmail.com
Thu May 30 14:44:42 CEST 2013

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

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)



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