[gmx-users] Pulling multiple groups

[Justin A. Lemkul]

Wright, Louise wrote:
> Hi
> I am trying to use the pull code of gromacs (version 4.5.5) to constrain 
> the com of a number of groups (labelled CIT, CIT1, CIT2...) to a 
> reference group (labelled GOLD).  This is the segment of the .mdp file I 
> have used:
> 
> ;CoM pull calculations
> pull                    = constraint
> pull_geometry           = distance
> pull_dim                = N N Y
> pull_constr_tol         = 1e-6
> ; add COM distance of starting config to pull_init
> pull_start              = yes
> ;frequency for writing COMS of all pull group
> pull_nstxout            = 10
> ;frequency for writing force of all pull group
> pull_nstfout            = 10
> pull_ngroups            = 12
> ;name of reference group
> pull_group0             = GOLD
> pull_group1             = CIT
> pull_group2             = CIT1
> pull_group3             = CIT2
> pull_group4             = CIT3
> pull_group5             = CIT4
> pull_group6             = CIT5
> pull_group7             = CIT6
> pull_group8             = CIT7
> pull_group9             = CIT8
> pull_group10            = CIT9
> pull_group11            = CIT10
> pull_group12            = CIT11
> ;reference distance at t=0 (nm)
> pull_rate1              = 0
> pull_rate2              = 0
> pull_rate3              = 0
> pull_rate4              = 0
> pull_rate5              = 0
> pull_rate6              = 0
> pull_rate7              = 0
> pull_rate8              = 0
> pull_rate9              = 0
> pull_rate10              = 0
> pull_rate11             = 0
> pull_rate12             = 0
> 
> However, when I look at the output only the first pull group (CIT) is 
> being restrained at a constant com height from GOLD.  The others move away.
> 
> output from pullx.xvg:
> 0.0400  0.717773        0.984186        0.977682        0.979256        
> 0.975962        0.978739        0.974255        0.969942        0.97706 
> 0.987668        1.00157 0.979894        0.982414
> 0.0500  0.717776        0.985442        0.977141        0.979625        
> 0.976002        0.978158        0.973563        0.968578        0.97746 
> 0.989067        1.00363 0.980026        0.983273
> 0.0600  0.717776        0.986709        0.976605        0.980068        
> 0.976034        0.977671        0.973037        0.967893        
> 0.977855        0.990371        1.00531 0.980148        0.984034
> 0.0700  0.717776        0.987965        0.976222        0.98048 
> 0.976129        0.977231        0.972626        0.967535        
> 0.978239        0.991569        1.00703 0.980298        0.984731
> 0.0800  0.717776        0.989129        0.976023        0.980946        
> 0.976285        0.976717        0.972257        0.967184        
> 0.978667        0.99272 1.0089  0.980504        0.985445
> 0.0900  0.717776        0.990186        0.97597 0.98157 0.976445        
> 0.976252        0.971888        0.966841        0.97909 0.993944        
> 1.01091 0.980784        0.986181
> 0.1000  0.717776        0.991179        0.976024        0.982275        
> 0.9766  0.975847        0.971445        0.966549        0.979437        
> 0.995328        1.01311 0.98115 0.986935
> 0.1100  0.717776        0.992167        0.976165        0.982984        
> 0.976787        0.975344        0.970858        0.966275        
> 0.979715        0.996957        1.01556 0.981619        0.987732
> 
> I was wondering what I have done wrong in the input .mdp file.  >From 
> looking at the manual, I can't work it out since I think I have set it 
> up as shown.
> 

Do the distances continually get larger?  I see no clear evidence of that here, 
but it is a short timeframe.  The COM separation will fluctuate to a small 
extent; you should not expect the distance to remain absolutely fixed.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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