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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