[gmx-users] How to define pull-init for two pull groups

[Justin Lemkul]

On 1/14/14, 8:23 PM, Rini Gupta wrote:
> Dear gmx-users,
>
> Thanks for the nice reply.
>
> I have corrected the pull code as:
>
>
>
> ; Pull code
> pull            = umbrella
> pull_geometry   = position  ;
> pull_dim        = N N Y
> pull_start      = yes        ; define initial COM distance > 0
> pull_ngroups    = 2
> pull_group0     = cbilayer  ; center of carbon's of bilayer
> pull_group1     = phosup   ; phosphate atom of 16th PEPC in top
> pull_pbcatom1   = 0
> pull_vec1       = 0.0 0.0 -1.0
> pull_init1      = 0 0 0
> pull_rate1      = 0.01      ; 0.01 nm per ps = 10 nm per ns
> pull_k1         = 1000      ; kJ mol^-1 nm^-2
> pull_group2     = phoslow   ; phosphate atom of 56th PEPC in bottom
> pull_pbcatom2   = 0
> pull_vec2       = 0.0 0.0 1.0
> pull_init2      = 0 0 0
> pull_rate2      = 0.01      ; 0.01 nm per ps = 10 nm per ns
> pull_k2         = 1000      ; kJ mol^-1 nm^-2
>
> Now, after extracting trajectory frames and measuring the distances between
> COM distances between two pull groups and a reference group, I found that
> values of summary_distances.dat are first decreasing through roughly half
> of the frames and then start increasing till final frame.
> The snapshots are also matching the output.
>   If  this is right for a lipid crossing through bilayer then in order to
> generate starting configurations at windows spacing of 0.06 nm I ran the
> script (setup-umbrella.py) link provided in tutorial.
> But, the output file (caught_output.txt) which contain the list of initial
> frames with distances
> select only frames after half of the times frames.
> i.e If I provide a .dat file corresponding to 400 time frames it produces
> the list of frames at a desired spacing excluding the frames where distance
> between reference and pull group is decreasing . I got :
>
> Creating frame-specific output for files:
> run-umbrella.sh
>       frame      dist    d_dist
>           0     3.082        NA
>           6     3.137     0.055
>         222     3.215     0.078
>         224     3.272     0.057
>         228     3.320     0.049
>         230     3.380     0.060
>         231     3.427     0.047
>         237     3.495     0.068
>         239     3.557     0.062
>         240     3.619     0.062
>         242     3.720     0.102
>         257     3.781     0.061
>         271     3.835     0.053
>         272     3.894     0.059
>         283     3.935     0.041
>         286     4.010     0.075
>         288     4.063     0.053
>         299     4.113     0.049
>         300     4.188     0.075
>         302     4.243     0.055
>         305     4.303     0.060
>         311     4.397     0.094
>         312     4.431     0.034
>
>
> If this is case, how it will generate a sufficient overlap between adjacent
> windows ?
>
> Also, script works only for single lipid pulling out of a layer. It is
> possible to use it for two lipids simultaneously crossing the bilayer in
> different directions.
>

Don't try to apply the scripts in the tutorial too literally.  You're doing 
something much more complex than what the tutorial did and what those scripts 
are designed for.  You can apply the same logic, but will probably have to come 
up with your own scripts to extract pertinent information.

-Justin

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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