[gmx-users] constant_force pulling

Berk Hess gmx3 at hotmail.com
Wed Nov 18 20:09:12 CET 2009


I think you mis-read the manual.
With constant-force there is no reference position (since a linear potential has no reference point),
but you can, and in your case should, use a reference group.
Then you can also use the geometry distance.


> Date: Wed, 18 Nov 2009 19:08:43 +0100
> From: schlesi at uni-mainz.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] constant_force pulling
> Hi all,
> i tried out the constant_force pulling, to simulate a force clamp 
> pulling experiment. But there are now some questions. But first describe 
> the system and so on...
> The system consists of two molecules which can bind through hydrogen 
> bonds with no water. Each molecule has one atom which will be consibered 
> for the pulling. ZUG is that from the molecule that should be pulled and 
> REF is the one from the other molecule (in umbrella pulling it would be 
> the reference group). So the system looks the following
> REF----hbonds-----ZUG         ->   pulling in this direction.
> In the *.mdp file i had the following parameters:
> pull                =  constant_force
> pull_geometry       =  direction
> pull_dim            =  Y Y Y
> pull_ngroups        =  1
> pull_group1         =  ZUG
> pull_k1             =  -500
> pull_vec1           =  1.631 0.196 0.279
> where pull_vec1 is the vector from REF to ZUG.
> The manual states that for constant_force there is no reference group, 
> so i took for pull_geometry direction, because it looks like that all 
> the other options need a reference group.
> grompp complained that the pulling is in absolute coordinates and that 
> this can lead to artefacts (i think when the molecule starts to rotate). 
> In the end both molecule were pulled together through space, because REF 
> wasn't fixed (so the molecule could move freely).
> Then i fixed the position of REF via position restraints and a freeze 
> group (not both together, were two simulations). In both cases grompp 
> didn't complain about the pulling in absolute coordinates. (I fixed the 
> position of REF, because that's the same what the pullcode does in 
> umbrella/position pulling with the reference group, the spring moves 
> relative to the reference group so the reference group is fixed for the 
> pulling).
> So now to my questions:
> 1) Would this (to fix the position of REF) be the right way to simulate 
> a force clamp experiment?
> 2) If so, what would be better for fixing freeze group or position 
> restraint? I tend to the former because then REF is fixed totally, in 
> the later cases the two molecule would move a little bit, till the force 
> from the pulling and restraint will be equilibrated and then i have 
> nearly the same case as in the freeze group, but REF could fluctuate in 
> space (how much depends on the strength of the restraints, but i think 
> it would not be very much).
> 3) What to do with COM? Remove nothing, or only the translation or 
> translation and rotation? One remark, i disabled the pbc, but i would be 
> interesed what one should use best without and with pbc (in the later 
> cases there could be also water present).
> Hope somebody has any ideas.
> Greetings
> Thomas
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