[gmx-users] hi

[Idriz Seferi]

Hi all,

I have a question regarding Umbrella Sampling in gromacs 5.1.

I am following the tutorial of Dr. Lemkul () and I am getting errors about
the parameters when I am running gmx grompp.
Specifically, I am constantly getting an error on the pull-rate option.

Dr. Lemkul uses the following options for the pull code:

; Pull code
pull                    = yes
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = Chain_A
pull_group2_name        = Chain_B
pull_coord1_type        = umbrella      ; harmonic biasing force
pull_coord1_geometry    = distance      ; simple distance increase
pull_coord1_groups      = 1 2
pull_coord1_dim         = N N Y
pull_start              = yes           ; define initial COM distance > 0
pull_rate1              = 0.0
pull_k1                 = 1000          ; kJ mol^-1 nm^-2

However, when I run gmx grompp with these parameters I get a warning on
pull_start, pull_rate1, and pull_k1. With the help of the gromacs webpage
on mdp options, I modified the above list to the following:

pull                     = yes
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = Chain_A
pull_group2_name        = Chain_B
pull_coord1_type        = umbrella      ; harmonic biasing force
pull_coord1_geometry    = distance      ; simple distance increase
pull_coord1_groups      = 1 2
pull_coord1_dim         = N N Y
pull_start              = yes           ; define initial COM distance > 0
pull_coord1_rate        = 0.0          ; 0.01 nm per ps = 10 nm per ns
pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2