[gmx-users] GMX 2018 and 'distance' pull

[Justin Lemkul]

On 3/13/18 2:38 AM, Alex wrote:
> Hi all,
>
> There seems to be a problem with the new pull code when it comes to 
> using it for umbrella sampling with 'distance' directive for WHAM (the 
> original thread is my earlier exchange with Justin in '[gmx-users] 
> seeming paradox with gmx wham'). In order to subdue unknown statement 
> errors, the code was modified to:
>
> pull                 = yes
> pull-coord1-type     = umbrella
> pull_ngroups            = 2
> pull_ncoords            = 1
> pull_group1_name        = K
> pull_group2_name        = CNT
> pull_coord1_geometry    = distance
> pull_coord1_groups      = 1 2
> pull-coord1-dim         = Y Y Y
> pull_coord1_rate        = 0.0
> pull_coord1_k           = 1000
> pull_coord1_start       = yes
>
> But it is a mess anyway. The box is 5.7 nm tall (6 nm by 5.5 nm wide) 
> and the membrane's COM is definitely close to the geometric center of 
> the box and it is definitely not moving beyond a few angstroms from 
> thermal fluctuations (the membrane is very strongly restrained at its 
> perimeter). The initial coordinate configurations for the other group 
> (an ion) are a sweep of heights between -1.5 nm and 1.5 nm right 
> relative to the membrane's COM along the height -- initial x and y are 
> those of the membrane's COM -- see my very angry drawing here: 
> https://www.dropbox.com/s/bwugqp5v9qt7iaq/pull.jpg?dl=0   :) The 
> distance simply cannot exceed 1.5 nm with spherical symmetry, it just 
> can't. And yet, i get errors like
>
> "Distance between pull groups 1 and 2 (3.035939 nm) is larger than 
> 0.49 times the box size (2.728418)." -- this is from grompp
>
> Sometimes grompp is actually satisfied, but then mdrun throws this 
> after a few thousand steps:
>
> "Program:     gmx mdrun, version 2018
> Source file: src/gromacs/pulling/pull.cpp (line 707)
> MPI rank:    0 (out of 2)
>
> Fatal error:
> Distance between pull groups 1 and 2 (2.732163 nm) is larger than 0.49 
> times
> the box size (2.728418)."
>
> This does not seem possible, because at this point the ion is radially 
> restrained (1000 kJ/mol/nm2). This was /never/ an issue with 5.0.4 
> with a considerably smaller box (4 nm) -- the entire mdp file is a 
> copy of what worked in 5.0.4, except the pull code is as above. Do I 
> just continue increasing the box size?
>

You may have a situation that requires manual assignment of 
pull_group1_pbcatom1, as the automatic choice of "choose a number in the 
middle of the list" may be inappropriate in your case. It works well for 
a globular protein, but for a sheet of material, probably you're getting 
an incorrect check from mdrun.

The pull code was basically re-written in version 5.1, hence why you may 
not have seen an issue back in 5.0.4.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
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jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

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