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

Berk Hess gmx3 at hotmail.com
Thu Jan 29 08:06:37 CET 2009 

Hi,

This issue has been resolved.
It was indeed a problem of a pull group consisting of multiple molecules.
In this case the choice of the pull_pbcatom mdp parameter was critical.
If you do not set this, it takes the numerically middle atom of the group.
In this case that was an atom in a lipid head group.
The distance of this reference head group atom to the head groups
on the other side of the bilayer was shorter through pbc and the solvent
than through the bilayer.
Setting pull_pbcatom by hand to a tail end atom resolved the issue.

Berk

From: gmx3 at hotmail.com
To: gmx-users at gromacs.org
Subject: RE: [gmx-users] Transition difficulties: version 3.3.3	to	4.0.3	regarding pull_geometry=distance
Date: Wed, 28 Jan 2009 10:45:33 +0100








Hi,

You can mail the system to me.
Please include all the details required to run the system
and the different results you get with the exact Gromacs version numbers.

Berk

> Date: Wed, 28 Jan 2009 00:52:06 -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,
> 
> The permeants in my bilayer system are improperly pulled in calculations 
> using all versions of Gromacs 4.0.x including the VERSION 
> 4.0.99_development_20090120.  Since, due to restrictions, I can not 
> provide the topology file for my system to bugzilla, I constructed a 
> similar prototypical system using Prof. Tieleman's POPC bilayer 
> coordinates and field parameters.  A buckyball permenat doped in the 
> center of this system did indeed react similarly in a 4.0.3 calculation 
> with an improper pull away from the equilibrated 3.3.1 constraint force 
> coordinates.  It was heartening to see that this problem was fixed for 
> that system, by using VERSION 4.0.99_development_20090120.  
> Unfortunately, again the problem remained for my actual system, even 
> with use of the newest version of code.
> 
> Since the cylinder option is now operational, I have a viable 
> work-around for this problem.  I am quite appreciative of the attention 
> that this issue has received.  If there is continued interest, and a 
> willingness for an engineer to receive the topology file in a less 
> public forum than bugzilla, I believe we could proceed with the 
> debugging process.
> 
> Thank you,
> 
> Steve Fiedler
> 
> 
> 
> 
> Berk Hess wrote:
> > Hi,
> >
> > Just to be sure, the pull code is producing the correct results now?
> > The only problems should be in several analysis tools.
> >
> > The analysis tools have been written only with analysis of molecules
> > or parts of molecules in mind. When you want to analyze groups
> > that cover two molecules or more there will be pbc problems.
> > These are not simple to fix. If the distances between all the atoms
> > in the group are less than half a box length there is a unique COM.
> > The procedure should be similar to what trjconv -pbc cluster does.
> >
> > I can try to implement this for g_traj and g_dist.
> > Are there other tools that cause problems?
> >
> > Berk
> >
> > > Date: Mon, 26 Jan 2009 17:46:26 -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 Chris,
> > >
> > > Your suggestions were helpful. Due to the nature of this problem, there
> > > were limitations in the application of the sequence of steps that you
> > > recommended. Specifically, the difference in the equilibrated structure
> > > from version 3.3.x to the calculated reference center of mass from
> > > version 4.0.x causes an unreasonable "jump" with constraint force
> > > calculation. Resultant bad contacts prohibit generation of a pull
> > > output file.
> > >
> > > More generally though, I believe I understand your broader point: the
> > > sensitive nature of the periodic box with respect to the pull code and
> > > possible discrepancies in the pbc treatment by various utilities, may
> > > cause confusion with the diagnostic process. The test bilayer system I
> > > created however, centered distantly from the x and y box edges, may
> > > effectively remove this set of concerns. For example, this
> > > configuration is relatively unchanged upon "recentering", however it is
> > > still susceptible to the problem that is the subject of this discussion.
> > >
> > > If I can reproduce this phenomenon with a publicly available topology
> > > file, I can provide the necessary input files for inspection.
> > >
> > > Thank you again,
> > >
> > > Steve Fiedler
> > >
> > >
> > >
> > > chris.neale at utoronto.ca wrote:
> > > > Hi Steve,
> > > >
> > > > what I intended to suggest was actually something different (and much
> > > > easier).
> > > >
> > > > The idea is not that you need some special system to be able to
> > > > utilize the pull code, but that the pull code is correct whereas the
> > > > g_dist and g_traj programs are not as good at treating pbc in the way
> > > > that one desires.
> > > >
> > > > I suggest the following.
> > > >
> > > > 1. Take your original system and run the pull code for a very short
> > > > simulation. Use the last line of the output to calculate the relevant
> > > > displacement
> > > >
> > > > 2. Now use trjconv -b -e to get the last frame of the .xtc that
> > > > resulted from that short MD run as a .gro file, call it final.gro. I
> > > > suspect that your groups are not entirely in the same simulation box
> > > > in final.gro.
> > > >
> > > > 3. Now make a new .ndx file from that .gro and give it a single
> > > > residue that is near your binding pocket, call it R_1
> > > >
> > > > 4. Now apply trjconv -center -pbc mol -ur compact while selecting R_1
> > > > for centering, call the new .gro file final_center.gro
> > > >
> > > > 5. Visualize final_center.gro and ensure that all of your relevant
> > > > atoms are in the same image in the way that puts the minimum distance
> > > > between them along a path that is entirely contained within the unit
> > > > cell. If not, go back to step 3 and try making a group R_2, etc.
> > > > until this process works. NOTE: you might think that giving trjconv
> > > > -center the relevant groups that you use for pulling will be a good
> > > > idea here, but it is not. The problem there is that the atoms may be
> > > > "centered" by placing half on the left boundary and half on the right
> > > > boundary. I find using one logically selected residue or atom is the
> > > > best method here.
> > > >
> > > > 6. Assuming that you got what you wanted in step 5, now run g_traj 
> > and
> > > > g_dist on final_center.gro. In my case, I found that g_traj and 
> > g_dist
> > > > give the same answer as the pull code output when I am using
> > > > final_center.gro, but not always when I am using final.gro.
> > > >
> > > > *** I always laugh when these problems arise because, in an important
> > > > sense, the protein *did* jump out of the simulation box... at 
> > least as
> > > > far as g_traj and g_dist are concerned. This, we must hope, is
> > > > correctly treated in the pull code even though it is incorrectly (or
> > > > at least unintuitively) treated by g_traj and g_dist.
> > > >
> > > > Chris.
> > > >
> > > > -- original message --
> > > >
> > > > 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
> > > >
> > > > _______________________________________________
> > > > 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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