[gmx-users] hi

[Barnett, James W]

On Sun, 2015-09-13 at 21:41 -0600, Idriz Seferi wrote:
> 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.

'pull-rate1' should be 'pull-coord1-rate'

> 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
> > 
> > 
> > 
> > 

-- 
James “Wes” Barnett, Ph.D. Candidate
Louisiana Board of Regents Fellow

Chemical and Biomolecular Engineering
Tulane University
341-B Lindy Boggs Center for Energy and Biotechnology
6823 St. Charles Ave
New Orleans, Louisiana 70118-5674
jbarnet4 at tulane.edu