If you think this is a bug introduced in gromacs 2018, perhaps you could
file a bug report on https://redmine.gromacs.org/? Attaching tpr's (or run
setups) both for the 2018 and the 5.04 version together with an md.log
would be helpful.
On Tue, Mar 13, 2018 at 7:38 AM, Alex <nedoma...@gmail.com> 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
> 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?
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