[gmx-users] hi

[Justin Lemkul]

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On 9/13/15 11:35 PM, Idriz Seferi 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
>

These modifications look correct to me.  I have fixed them in the tutorial 
(sorry for the typos; working too quickly).  What is the specific error grompp 
raises when using these (copied and pasted, please)?

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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