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

[Berk Hess]

Hi,

I think g_clustsize requires a different algorithm.
Here you don't know a priori what the group is.
I guess things are easier here, since you always cluster
(parts of) molecules. Or am I wrong?

I am not familiar with this program.
If there are problems, please file a bugzilla.

Berk

Date: Tue, 27 Jan 2009 09:58:32 +0100
From: r.friedman at bioc.uzh.ch
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Transition difficulties: version 3.3.3	to	4.0.3	regarding pull_geometry=distance






  


Dear Berk,



I think that g_clustsize has a similar problem. IIRC I fixed it in a
similar way on my own copy.

There are probably other tools that will suffer from this as well, but
for g_clustsize it's important because it may deal with such groups.



Same goes for trjconv, e.g., for a protein and ligand. 



Ran.



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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> > 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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