[gmx-users] RE: 2D umbrella sampling simulation

mjyang mjyang at hku.hk
Fri Oct 25 05:42:15 CEST 2013

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.

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Christopher Neale [chris.neale at mail.utoronto.ca]
Sent: Friday, October 25, 2013 4:44 AM
To: gmx-users at 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.


-- 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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