Hi Chris,
Your suggestions were helpful. Due to the nature of this problem, there
were limitations in the application of the sequence of steps that you
recommended. Specifically, the difference in the equilibrated structure
from version 3.3.x to the calculated reference center of mass from
version 4.0.x causes an unreasonable "jump" with constraint force
calculation. Resultant bad contacts prohibit generation of a pull
output file.
More generally though, I believe I understand your broader point: the
sensitive nature of the periodic box with respect to the pull code and
possible discrepancies in the pbc treatment by various utilities, may
cause confusion with the diagnostic process. The test bilayer system I
created however, centered distantly from the x and y box edges, may
effectively remove this set of concerns. For example, this
configuration is relatively unchanged upon "recentering", however it is
still susceptible to the problem that is the subject of this discussion.
If I can reproduce this phenomenon with a publicly available topology
file, I can provide the necessary input files for inspection.
Thank you again,
Steve Fiedler
chris.ne...@utoronto.ca wrote:
Hi Steve,
what I intended to suggest was actually something different (and much
easier).
The idea is not that you need some special system to be able to
utilize the pull code, but that the pull code is correct whereas the
g_dist and g_traj programs are not as good at treating pbc in the way
that one desires.
I suggest the following.
1. Take your original system and run the pull code for a very short
simulation. Use the last line of the output to calculate the relevant
displacement
2. Now use trjconv -b -e to get the last frame of the .xtc that
resulted from that short MD run as a .gro file, call it final.gro. I
suspect that your groups are not entirely in the same simulation box
in final.gro.
3. Now make a new .ndx file from that .gro and give it a single
residue that is near your binding pocket, call it R_1
4. Now apply trjconv -center -pbc mol -ur compact while selecting R_1
for centering, call the new .gro file final_center.gro
5. Visualize final_center.gro and ensure that all of your relevant
atoms are in the same image in the way that puts the minimum distance
between them along a path that is entirely contained within the unit
cell. If not, go back to step 3 and try making a group R_2, etc.
until this process works. NOTE: you might think that giving trjconv
-center the relevant groups that you use for pulling will be a good
idea here, but it is not. The problem there is that the atoms may be
"centered" by placing half on the left boundary and half on the right
boundary. I find using one logically selected residue or atom is the
best method here.
6. Assuming that you got what you wanted in step 5, now run g_traj and
g_dist on final_center.gro. In my case, I found that g_traj and g_dist
give the same answer as the pull code output when I am using
final_center.gro, but not always when I am using final.gro.
*** I always laugh when these problems arise because, in an important
sense, the protein *did* jump out of the simulation box... at least as
far as g_traj and g_dist are concerned. This, we must hope, is
correctly treated in the pull code even though it is incorrectly (or
at least unintuitively) treated by g_traj and g_dist.
Chris.
-- original message --
Hi,
Thank you Berk and Chris for the suggestions.
To address the possibility that this issue is related to periodic
boundaries, I used two approaches:
1. The pull group of interest (permeant) was centered in the x-y plane
of the box using Chris' approach. I then used the genconf utility to
replicate my lipid box to a 9x9 grid in the x-y plane and removed all
but the center box. This generated the coordinates for a bilayer system
with all lipid molecules inside a box and intact. The discrepancy
between the grompp (version 4.0.3) output and distances as calculated by
g_traj (version 4.0.3) persist, 2.667 vs. 0.3996 nm.
2. I constructed a three atom system containing 2 reference atoms of
type A, and a "pull" atom of type B. Proper output from grompp was
observed for all coordinates of both the reference and pulled atoms,
include coordinates for atoms moved outside the box in the x-y plane.
The coordinate, topology, and run control parameter file are given below.
If there are additional suggestions, I would be greatly appreciative.
Thank you,
Steve Fiedler
-----------------
conf.gro
Three atoms
3
1AAA A 1 1.500 1.500 1.000
2AAA A 2 0.500 1.500 1.000
3BBB B 3 -1.500 1.500 1.700
3.00000 3.00000 3.00000
-----------------
index.ndx
[ System ]
1 2 3
[ Ref ]
1 2
[ Pulled ]
3
-----------------
grompp.mdp
title = ThreeAtoms
integrator = md
dt = 0.001
nsteps = 1
ns_type = grid
pbc = xyz
coulombtype = shift
rlist = 1.4
rcoulomb = 1.4
rvdw = 1.4
tcoupl = no
pcoupl = no
constraint_algorithm = shake
shake_tol = 1e-4
gen-vel = no
gen-temp = 0
nstxout = 1
nstvout = 0
nstfout = 0
pull = umbrella
pull_geometry = distance
pull_dim = N N Y
pull_start = no
pull_init1 = 0.7
pull_group0 = Ref
pull_group1 = Pulled
pull_k1 = 10000
-----------------
topology.top
; topology for two partially charged atoms
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.125 0.5
[ atomtypes ]
;name mass charge ptype sig eps
A 1000.0000 0.000 A 0.50000 9.90000
B 9.0000 0.000 A 0.30000 9.00000
[ nonbond_params ]
; i j func sig eps
[ moleculetype ]
AAAA 1
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 A 1 AAA A 1 0.000 1000.0000
[ moleculetype ]
BBBB 1
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 B 1 BBB B 1 0.000 9.00
[ system ]
; name
Three atoms
[ molecules ]
; name number
AAAA 2
BBBB 1
Chris Neale wrote:
I just checked similar simulations of mine and Berk's suggestion
accounts for similar discrepancies that I notice on a quick
evaluation where g_traj and g_dist fail to give me the same distance
as I obtain from the pull pos.xvg file. As Berk suggests, once I
first trjconv -center -pbc mol -ur compact (giving an appropriate
residue for centering that puts all relevant pulled atoms in the same
box) then g_traj and g_dist both give me the exact same answer as I
calculate based on pull pos.xvg. Chris -- original message -- Hi,
There could be a problem with periodic boundary conditions. Do you
have multiple molecules in a pull group, or broken molecules? In that
case the COM position of 3.3.3 and g_traj are both incorrect. The
pull code in 4.0 grompp and mdrun are (as far as I know) always
correct. Berk
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Steve Fiedler, Ph.D.
Research Fellow
Department of Mechanical Engineering
The University of Michigan
2024 G.G. Brown
2350 Hayward St.
Ann Arbor, MI 48109-2125
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