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

[mjyang]

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-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.

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.
--
gmx-users mailing list    gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists