[gmx-users] hi

[Idriz Seferi]

Continuation of email:

However, I still get a warning on pull-rate - which I don't understand.

Hope you can help me understand how to deal with the pull-rate so that
grompp recognizes it. If you require the full list of parameters in the mdp
file to solve the problem, then please let me know.
Any help would be immensely appreciated.

Thank you

On Sun, Sep 13, 2015 at 9:35 PM, Idriz Seferi <idrizseferi89 at gmail.com>
wrote:

> 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
>
>
>
>