[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance

Berk Hess gmx3 at hotmail.com
Mon Jan 26 09:59:09 CET 2009 

Hi,

Strange, I think I have really fixed all problems now.
All test systems work fine for me.

Can you file a bugzilla entry?
Please include all the files needed to run grompp
as well as the correct pull distance and the pull distance you obtained.

Berk

> Date: Sun, 25 Jan 2009 23:45:29 -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,
> 
> 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
> > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > Please search the archive at http://www.gromacs.org/search before
> > > > posting!
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> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > > >
> > > >
> > >
> > >
> > > --
> > > 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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> 
> -- 
> 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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