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

[Chenlin Lu]

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.


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