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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