[gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)

Justin A. Lemkul jalemkul at vt.edu
Fri Sep 9 19:31:26 CEST 2011

Shilpi Chaurasia wrote:
>  I am trying to pull apart two dimers of tubulin protein joined 
> together, to form two separate dimers by steered molecular dynamics 
> using Pull code. The objective is to separate the dimers by pulling 
> along one axis only (Y axis). I ran the simulation for 25 ps and it 
> accomplished well but while visualizing the trajectory in VMD, in the 
> very beginning (first frame), dimers are at distance which is much 
> greater than expected. I expected that in first frame they should not 
> have separated too much (i.e. in just 1 ps, they are at greater 
> distance) I guess this is unusual. Please let me know where I am doing 
> wrong? I have used the following pull code:

Actual numbers would help.  Is your initial configuration simply split across 
periodic boundaries?  If the initial distance is roughly equivalent to one of 
the box vectors, then that's the case.  Otherwise, please provide real data and 
check to make sure your pull groups are what you think they are.

> pull            = umbrella
> pull_geometry   = distance
> pull_dim        = N N Y

Note that you're not actually pulling along Y as you state above.  Here, you're 
pulling along Z.  Perhaps that's one issue.


> pull_start      = yes         
> pull_init1      = 0.0
> pull_ngroups    = 1
> pull_group0     = dimer_ref               ; reference group (based on 
> index file)
> pull_group1     = dimer_pull           ; pull group
> pull_rate1      = 0.1          
> pull_k1         = 1000         
> pull_nstfout    = 10          
> pull_nstxout    = 10
> best regards,
> Shilpi Chaurasia


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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