[gmx-users] pull code, help pulling monomers in the same direction

Nawel Mele nawel.mele at gmail.com
Fri Feb 1 11:38:54 CET 2019

Dear Gromacs users,

I would like to use the pull code to pull two monomer closer to each other.
I am a bit confused on which of the following parameters (in red) needs to
have a positive or negative sign to allow the pulling on the same
direction. I want to pull the Chain_B, corresponding the one monomer,
towards the Chain_A, corresponding to the second monomer. Does anyone
perform that before??

; Pull code

pull                    = umbrella

pull_geometry           = distance  ; simple distance increase

pull_dim                = N N Y     ; pull along z

pull_group0             = Chain_B

pull_group1             = Chain_A

pull_vec1               = 0.0 0.0 -1.0

pull_ngroups            = 1         ; two groups defining one reaction

pull_start              = yes       ; define initial COM distance > 0

pull_rate1              = -0.01      ; 0.01 nm per ps = 10 nm per ns due to
the minus sign it pulls to opposite direction

pull_k1                 =1000      ; kJ mol^-1 nm^-2

Many thanks in advance,




Dr Nawel Mele,
T: +33 (0) 634443794 (Fr)

+44 (0) 7704331840 (UK)

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