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

> Date: Thu, 22 Jan 2009 13:22:24 -0500
> From: fied...@umich.edu
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
> > Dear all,
> > I have encountered an odd behavior with use of the "pull_geometry = > distance" option of the pull code, upon transitioning from Gromacs > version 3.3.3 to version 4.0.3. It appears to be related to the center > of mass distances of the two pull groups, which has an effect of > abruptly displacing the coordinates of the less massive group. A > diagnostic is a discrepancy between the distances between the pull > groups from the preprocessor output in version 4.0.3, and the distance > between the groups as calculated using the difference of the groups' > centers of mass from the g_traj utility. For example, using the > coordinates of a system previously equilibrated with the constraint > force approach from version 3.3.3, the grompp output from version 4.0.3 is:
> > Pull group  natoms  pbc atom  distance at start     reference at t=0
> 0 2672 1336 > 1 60 6818 2.673 0.400 > > Using g_traj (4.0.3 version), the difference of the distance between the > center of masses of the two groups is: 0.39911 nm versus the 2.673 value > from above. > > This issue does not exist in previous versions of Gromacs including > version 3.3.3. In version 4.0.3, this behavior occurs for both > pull=umbrella and pull = constraint, on 32 and 64 bit architecture > systems, and in both single and double precision calculations. A test > of a two atom system determined that the pull_start option was not > appropriate. The pull options used in the mdp file are listed below, as > well as the contents of the ppa file which has worked previously. > > Suggestions would be appreciated,
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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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