[gmx-users] umbrella-drug

Justin A. Lemkul jalemkul at vt.edu
Sun Jan 29 14:55:20 CET 2012

parto haghighi wrote:
> Dear Justin
> thank you for your response
> here is my umbrella part of mdp file:
> ; Pull code
> pull                 = umbrella
> pull_geometry  = position  ; simple distance increase
> pull_dim        = N N Y
> pull_start      = yes       ; define initial COM distance > 0
> pull_ngroups    = 1
> pull_group0     = DRUG
> pull_group1     = LIPID
> pull_rate1       = 0.1      ; 0.01 nm per ps = 10 nm per ns
> pull_k1           = 1000      ; kJ mol^-1 nm^-2
> pull_init1        =  0 0 0
> pull_vec1        = 0 0 1
> I want to pull drug to lipid bilayer.when i run with this mdp i have
> this error: pull_vec1 can not be zero when pull position and non-zero
> pull_init1
> Could you please help me?!

Please copy and paste the full error message from the terminal.  I cannot find 
that error in the source, though I find two similar ones, both indicating 
something slightly different.

In any case, you've got several parameters that need changing for this to work. 
  First, with the "position" geometry, you do not need pull_dim, as the pulling 
direction is read from pull_vec1.  Second, in order to pull the drug closer to 
the membrane, you need a negative pull rate.  As it stands, you're telling mdrun 
to move the drug such that it causes a positive change in COM distance. 
Otherwise, use the positive pull_rate1 and a negative vector along which to do 
the pulling (pull_vec1); both approaches should achieve the same end.



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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