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

Berk Hess gmx3 at hotmail.com
Sun Nov 15 22:48:13 CET 2009


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.


> 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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