[gmx-users] How to deal with the negative reference distance while doing Umbrella Sampling using Gromcas?

[Justin Lemkul]

On 12/7/19 1:32 AM, Chenlin Lu wrote:
>
> Hi all,
>
>
> I am tring to pull a protein across a lipid bi-layer and calculate the PMF. While generating the configurations for further sampling, the protein get close to the bi-layer and stuck there when the distance of the COMs are close enough. The protein cann't cross the bi-layer. And an error "Pull reference distance for coordinate 1 is negative (-0.000000)" arose.
>
>
> I checked it on google and found one similar probelm. (https://gromacs.org-gmx-users.maillist.sys.kth.narkive.com/1ecXOQDz/about-pull-init-and-pull-start). There, Justin suggested to use  "pull_start = no" + "pull_init1= (COM distance)" . However, it seems it doesn't work for my system.
>

If your protein crosses the membrane and the value of the reaction 
coordinate changes sign, you can't use "distance" geometry. You'll need 
a different option - any of the others can be made to work.

-Justin

> I am using Gormacs 5.1.4 and below is my pull code:
>
>
> ; Pull code
> pull                    = yes
> pull_ncoords            = 1         ; only one reaction coordinate
> pull_ngroups            = 2         ; two groups defining one reaction coordinate
> pull_group1_name        = Protein
> pull_group2_name        = DPPC
> 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_coord1_rate        = -0.01      ; 0.01 nm per ps = 10 nm per ns
> pull_coord1_k           = 2000      ; kJ mol^-1 nm^-2
> pull_coord1_start       = yes       ; define initial COM distance > 0
> pull_coord1_init        =  0      ; define initial COM distance > 0
>
>
>
>
> Could you please give some advice? Thanks a lot in advance.
>
> --------------------------------------------------
>
> Chenlin Lu
>
> Department of Chemical Engineering,
>
> Tsinghua University, Beijing, 100084
>
> Tel: 86-13120180517
>
> Email: lucl17 at mails.tsinghua.edu.cn
>

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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