Dear Chris,
Thanks for your check. Yes, it should be pull_group2 for C. In this case,
the two distances have a reference group B. What about the case in which no
common reference group is shared with the two distances, e.g. distance1 is
defined as A-B and distance2 as C-D? Can current gromacs codes perform 2D
umbrella sampling for this problem?
Many thanks.
Mingjun
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf
Of Christopher Neale [chris.ne...@mail.utoronto.ca]
Sent: Friday, October 25, 2013 4:44 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] 2D umbrella sampling simulation
Your restraint involving group C should use pull_group2, etc, not another copy
of pull_group1. Other than that,
it looks like a valid approach.
Chris.
-- original message --
I am going to perform the two-dimensional umbrella sampling using a pair of
distances (the distance btw atoms A and B, C and B) in the restraints. Could
someone please tell whether I can use the current pull code as follows?
---------------------------------------------
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = Y Y Y
pull_start = no
pull_ngroups = 2
pull_group0 = B
pull_group1 = A ;restraint of distance btw A and B
pull_init1 = 2.7 ;equilibrium distance of A-B
pull_rate1 = 0.0
pull_k1 = 2000 ; kJ mol^-1 nm^-2
pull_group1 = C ;restraint of distance btw C and B
pull_init1 = 3.7 ;equilibrium distance of C-B
pull_rate1 = 0.0
pull_k1 = 2500 ; kJ mol^-1 nm^-2
pull_nstxout = 1000 ; every 2 ps
pull_nstfout = 1000 ; every 2 ps
-------------------------------------------------
Many thanks.
--
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