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

[Berk Hess]

Hi,

You should use pull_geometry=direction.
distances don't get negative.

Berk

> Date: Sat, 14 Nov 2009 09:21:39 -0500
> From: chris.neale at utoronto.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] pull code with defined negative relative displacements
> 
> Hello, I am re-running some of our gromacs 3 simulations using gromacs
> 4, and as far as I can tell the gromacs 4 pull code, while very nicely
> enhanced from gromacs 3, has also lost some functionality.
> 
> I am calculating the PMF of a peptide across a bilayer and, to  
> simplify the issue, what I can't figure out how to do with gromacs 4  
> is to pull group1 to a position 1 nm more negative along the z-axis  
> than group 0 (the bilayer in this case) for some replicas and to 1 nm  
> more positive along the z-axis than group 0 in others. I'll focus on  
> the negative displacement here as it is the one that is giving me  
> problems.
> 
> This used to be possible with the following gromacs 3 pull.ppa options:
> 
> runtype   = umbrella
> reftype   = com
> pulldim   = N N Y
> reference_group = group0
> group_1   = group1
> K1        = 500
> Pos1      = 0 0 -1.0
> 
> Sure, I could start group1 in the correct negative-z displacement from
> group0 and use pull_init1=+1.0, but this will not work when, for
> instance, I want to restrain it to -0.1 nm (using pull_init1=+0.1),
> where the sampling will infrequently jump back and forth about z=0.
> 
> Just to be sure, I tried for gromacs 4 are the following pull code  
> .mdp options:
> 
> pull                     = umbrella
> pull_geometry            = distance
> 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
> 
> where mdrun complains:
> "Pull reference distance for group 1 is negative (-1.000000)"
> 
> and it is pretty obvious why this doesn't work since it is asking for
> a negative displacement. Nevertheless, I tried it and pull_init1
> appears to get set to zero.
> 
> I also attempted the following.
> 
> pull                     = umbrella
> pull_geometry            = distance
> 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
> 
> where I would then use
> pull_init1 = 1.0
> pull_vec1  = 0 0 1
> for the positive side of the bilayer.
> 
> However, when I look at the forces, I am getting the negative of what  
> I should get when pull_vec1 = 0 0 -1.
> 
> coord.xvg:
> 610.0000	4.9343	-1.02019
> 660.0001	4.91454	-0.949747
> 
> force.xvg:
> 610.0000	-10.0932
> 660.0001	25.1265
> 
> Although I am getting exactly what I should get when pull_vec1 = 0 0 1  
> (for intended positive displacements).
> 
> coord.xvg:
> 660.0001	4.9014	1.16304
> 
> force.xvg:
> 660.0001	-81.5201
> 
> Any ideas are greatly appreciated. I can probably mod the code for my
> needs, but a standard gromacs binary is always preferable.
> 
> Thank you,
> Chris.
> 
> 
> 
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