[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Berk Hess
gmx3 at hotmail.com
Sat Jan 24 18:58:15 CET 2009
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,
> > _______________________________________________
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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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