[gmx-users] ull code with defined negative relative displacements

Berk Hess gmx3 at hotmail.com
Tue Nov 17 12:57:16 CET 2009


I would also like to be sure that everything works as I have intended it.
So I guess the following input should work:
pull                     = umbrella
pull_geometry            = direction
pull_dim                 = N N Y
pull_start               = no
pull_ngroups             = 1
pull_group0              = group0
pull_group1              = group1
pull_init1               = 1.0
pull_rate1               = 0
pull_k1                  = 500.0
pull_vec1                = 0 0 1
pull_init1 = -1.0

You can also make vec1 -1 and init1 1, but note that also f and dX in the pull output
files will then change sign.


> Date: Mon, 16 Nov 2009 01:45:32 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] ull code with defined negative relative displacements
> Thank you very much Berk,
> I'm not trying to be argumentative for arguments sake, but I just  
> can't see how exactly one would make pull_geometry=direction work in  
> this way. Although I think that I have shown the evidence for this in  
> my posts, if I am wrong here then clearly I misunderstand something  
> that is pretty important and, as such, I am keen to stick with this  
> thread.
> If you have the time to post the entire pull-code portion of the .mdp  
> options for a pull_geometry=direction run to harmonically restrain  
> group 1 at a position of 1 nm more negative z in reference to group 0  
> then I will do the testing for that setup.
> Nevertheless, I realize that you are very busy and may have more  
> pressing priorities.
> Thank you for all of your time sticking with this thread for so long,
> Chris.
> Hi,
> I would still say pull_geometry=direction would be the easiest  
> solution for this case,
> but pull_geometry=position will probably do the same thing.
> Berk
> [Hide Quoted Text]
> Date: Sun, 15 Nov 2009 17:11:43 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] pull code with defined negative relative displacements
> Hi Berk,
> I do not mean the box 0, and I am aware about the pull distance
> needing to be less than half of the smallest box length. Please allow
> me describe a bit more rigorously what I need to avoid. I will use an
> example that is totally fictitious, but is designed to emphasize the
> bimodal sampling issue that is relevant to my actual study.
> 1. Imagine that one wants to calculate the PMF for a water molecule
> along the normal to an asymmetric bilayer in which one leaflet is POPC
> and the other is lipidA.
> 2. The free energy for that water residing 0.1 nm away from the
> bilayer center in the POPC leaflet (call it -0.1 nm from the bilayer
> center) needs to be calculated separately from the free energy for
> that water residing 0.1 nm away from the bilayer center in the lipidA
> leaflet (call it +0.1 nm from the bilayer center).
> 3. Let the force constant be 500 kJ/mol/nm^2 and let the user apply
> pull_geometry=distance and pull_init1=0.1 while starting the replica
> at 0.1 nm from the bilayer center in two simulations where one takes
> (a) a starting water position that is 0.1 nm toward the POPC
> headgroups and the other takes (b) a starting position of the water to
> be 0.1 nm toward the lipidA headgroups.
> 4. I posit that the probability distributions of the water about the
> bilayer normal from simulations (a) and (b) in part 3 above will
> converge to the same distribution and that this distribution will be
> bimodal with one peak at -0.1 nm and one peak at +0.1 nm. This is
> because the simulation that started at -0.1 (0.1 nm closer to the POPC
> headgroups) will, even under the biasing force, infrequently cross the
> bilayer center of mass and then be closer to the lipidA heagroups. At
> this point. the direction of the applied force will the change to draw
> the water toward the other possible location at +0.1 nm.
> 5a. For displacements >> 0.1 nm, this will not be a problem.
> 5b. For larger force constants, this will not be a problem at 0.1 nm,
> but will still be a problem for some closer centers of restraint.
> 6. pull_geometry=distance is entirely incompatible with this approach.
> 7. pull_geometry=position does appear to work.
> Thanks for your patience,
> Chris.
> -- original message --
> Hi,
> Sorry, but I have no clue what you mean with sampling >0
> and how you would end up with a bimodal distribution.
> You don't mean the box 0, do you?
> That is irrelevant.
> What can be a problem is that you pull distance should not be more
> than half the box length.
> Berk
> Date: Sun, 15 Nov 2009 12:33:30 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] pull code with defined negative relative displacements
> I only now noticed Justin mail on g_wham.
> You can probably also use pull_geometry=distance and pull_init=1,
> if you starting structure has group1 close to 1 nm below group 0.
> Agreed, although this will not work when the force constant is not
> strong enough to inhibit any sampling >0 -- wherein the distribution
>    about 0 would become bimodal and this is something that I can not
> allow.
> As far as I can tell, pull_geometry=position, pull_init1<0, and
> pull_vec1=0 0 0 is the solution, as per my previous message.
> Thank you,
> Chris.
> -- 
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