On 3/13/18 7:16 AM, Justin Lemkul wrote:
On 3/13/18 2:38 AM, Alex wrote:
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)
Distance between pull groups 1 and 2 (2.732163 nm) is larger than
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
Sorry, that should be pull_group1_pbcatom. Must remind myself not to
email before coffee...
Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
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