[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Steve Fiedler
fiedler at umich.edu
Mon Jan 26 05:45:29 CET 2009
Hi,
I rebuilt the code using both sets of Berk's corrections. On an
isolated bilayer system with no periodic boundaries in the x-y plane
prepared in the manner previously explained, the recompiled grompp
output yielded no improvement in the discrepancies of the position of a
buckyball permeant. By visual inspection, it appears that the 4.0.x
versions still attempt to distort the position of the permeant
significant upward from the bilayer center, i.e., the center of mass of
the reference group. Interestingly, the 3.3.x and 4.0.x version
identically treated a test bilayer system constructed with a single
dummy particle permeant.
I appreciate the help of Berk, and Chris' detailed suggestions with this
interesting problem.
Sincerely,
Steve Fiedler
Berk Hess wrote:
> Hi,
>
> I just found out that I introduced a bug in 4.0.3, which could cause
> the pull code to crash or give wrong results when running single
> processor.
> In parallel it is correct.
> I committed fixed for 4.0.4.
>
> If you run in parallel things should be correct,
> or change in src/kernel/md.c:
> if (ir->pull) {
> dd_make_local_pull_groups(NULL,ir->pull,mdatoms);
> to
> if (ir->pull && PAR(cr)) {
> dd_make_local_pull_groups(NULL,ir->pull,mdatoms);
>
> Berk
>
> > Date: Fri, 23 Jan 2009 12:14:43 -0500
> > From: fiedler at umich.edu
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to
> 4.0.3 regarding pull_geometry=distance
> >
> > 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: fiedler at umich.edu
> > >> > To: gmx-users at 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,
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
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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
> >
> >
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
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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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