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Dear Berk,<br>
<br>
I think that g_clustsize has a similar problem. IIRC I fixed it in a
similar way on my own copy.<br>
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.<br>
<br>
Same goes for trjconv, e.g., for a protein and ligand. <br>
<br>
Ran.<br>
<br>
Berk Hess wrote:
<blockquote cite="midBLU134-W4655D9F9C18984D4875C718ECB0@phx.gbl"
type="cite">
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</style>Hi,<br>
<br>
Just to be sure, the pull code is producing the correct results now?<br>
The only problems should be in several analysis tools.<br>
<br>
The analysis tools have been written only with analysis of molecules<br>
or parts of molecules in mind. When you want to analyze groups<br>
that cover two molecules or more there will be pbc problems.<br>
These are not simple to fix. If the distances between all the atoms<br>
in the group are less than half a box length there is a unique COM.<br>
The procedure should be similar to what trjconv -pbc cluster does.<br>
<br>
I can try to implement this for g_traj and g_dist.<br>
Are there other tools that cause problems?<br>
<br>
Berk<br>
<br>
> Date: Mon, 26 Jan 2009 17:46:26 -0500<br>
> From: <a class="moz-txt-link-abbreviated" href="mailto:fiedler@umich.edu">fiedler@umich.edu</a><br>
> To: <a class="moz-txt-link-abbreviated" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> Subject: Re: [gmx-users] Transition difficulties: version 3.3.3 to
4.0.3 regarding pull_geometry=distance<br>
> <br>
> Hi Chris,<br>
> <br>
> Your suggestions were helpful. Due to the nature of this problem,
there <br>
> were limitations in the application of the sequence of steps that
you <br>
> recommended. Specifically, the difference in the equilibrated
structure <br>
> from version 3.3.x to the calculated reference center of mass from
<br>
> version 4.0.x causes an unreasonable "jump" with constraint force <br>
> calculation. Resultant bad contacts prohibit generation of a pull <br>
> output file.<br>
> <br>
> More generally though, I believe I understand your broader point:
the <br>
> sensitive nature of the periodic box with respect to the pull code
and <br>
> possible discrepancies in the pbc treatment by various utilities,
may <br>
> cause confusion with the diagnostic process. The test bilayer
system I <br>
> created however, centered distantly from the x and y box edges,
may <br>
> effectively remove this set of concerns. For example, this <br>
> configuration is relatively unchanged upon "recentering", however
it is <br>
> still susceptible to the problem that is the subject of this
discussion.<br>
> <br>
> If I can reproduce this phenomenon with a publicly available
topology <br>
> file, I can provide the necessary input files for inspection.<br>
> <br>
> Thank you again,<br>
> <br>
> Steve Fiedler<br>
> <br>
> <br>
> <br>
> <a class="moz-txt-link-abbreviated" href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a> wrote:<br>
> > Hi Steve,<br>
> ><br>
> > what I intended to suggest was actually something different
(and much <br>
> > easier).<br>
> ><br>
> > The idea is not that you need some special system to be able
to <br>
> > utilize the pull code, but that the pull code is correct
whereas the <br>
> > g_dist and g_traj programs are not as good at treating pbc in
the way <br>
> > that one desires.<br>
> ><br>
> > I suggest the following.<br>
> ><br>
> > 1. Take your original system and run the pull code for a very
short <br>
> > simulation. Use the last line of the output to calculate the
relevant <br>
> > displacement<br>
> ><br>
> > 2. Now use trjconv -b -e to get the last frame of the .xtc
that <br>
> > resulted from that short MD run as a .gro file, call it
final.gro. I <br>
> > suspect that your groups are not entirely in the same
simulation box <br>
> > in final.gro.<br>
> ><br>
> > 3. Now make a new .ndx file from that .gro and give it a
single <br>
> > residue that is near your binding pocket, call it R_1<br>
> ><br>
> > 4. Now apply trjconv -center -pbc mol -ur compact while
selecting R_1 <br>
> > for centering, call the new .gro file final_center.gro<br>
> ><br>
> > 5. Visualize final_center.gro and ensure that all of your
relevant <br>
> > atoms are in the same image in the way that puts the minimum
distance <br>
> > between them along a path that is entirely contained within
the unit <br>
> > cell. If not, go back to step 3 and try making a group R_2,
etc. <br>
> > until this process works. NOTE: you might think that giving
trjconv <br>
> > -center the relevant groups that you use for pulling will be
a good <br>
> > idea here, but it is not. The problem there is that the atoms
may be <br>
> > "centered" by placing half on the left boundary and half on
the right <br>
> > boundary. I find using one logically selected residue or atom
is the <br>
> > best method here.<br>
> ><br>
> > 6. Assuming that you got what you wanted in step 5, now run
g_traj and <br>
> > g_dist on final_center.gro. In my case, I found that g_traj
and g_dist <br>
> > give the same answer as the pull code output when I am using <br>
> > final_center.gro, but not always when I am using final.gro.<br>
> ><br>
> > *** I always laugh when these problems arise because, in an
important <br>
> > sense, the protein *did* jump out of the simulation box... at
least as <br>
> > far as g_traj and g_dist are concerned. This, we must hope,
is <br>
> > correctly treated in the pull code even though it is
incorrectly (or <br>
> > at least unintuitively) treated by g_traj and g_dist.<br>
> ><br>
> > Chris.<br>
> ><br>
> > -- original message --<br>
> ><br>
> > Hi,<br>
> ><br>
> > Thank you Berk and Chris for the suggestions.<br>
> ><br>
> > To address the possibility that this issue is related to
periodic<br>
> > boundaries, I used two approaches:<br>
> > 1. The pull group of interest (permeant) was centered in the
x-y plane<br>
> > of the box using Chris' approach. I then used the genconf
utility to<br>
> > replicate my lipid box to a 9x9 grid in the x-y plane and
removed all<br>
> > but the center box. This generated the coordinates for a
bilayer system<br>
> > with all lipid molecules inside a box and intact. The
discrepancy<br>
> > between the grompp (version 4.0.3) output and distances as
calculated by<br>
> > g_traj (version 4.0.3) persist, 2.667 vs. 0.3996 nm.<br>
> > 2. I constructed a three atom system containing 2 reference
atoms of<br>
> > type A, and a "pull" atom of type B. Proper output from
grompp was<br>
> > observed for all coordinates of both the reference and pulled
atoms,<br>
> > include coordinates for atoms moved outside the box in the
x-y plane.<br>
> > The coordinate, topology, and run control parameter file are
given below.<br>
> ><br>
> > If there are additional suggestions, I would be greatly
appreciative.<br>
> ><br>
> > Thank you,<br>
> ><br>
> > Steve Fiedler<br>
> ><br>
> > -----------------<br>
> > conf.gro<br>
> > Three atoms<br>
> > 3<br>
> > 1AAA A 1 1.500 1.500 1.000<br>
> > 2AAA A 2 0.500 1.500 1.000<br>
> > 3BBB B 3 -1.500 1.500 1.700<br>
> > 3.00000 3.00000 3.00000<br>
> > -----------------<br>
> > index.ndx<br>
> > [ System ]<br>
> > 1 2 3<br>
> > [ Ref ]<br>
> > 1 2<br>
> > [ Pulled ]<br>
> > 3<br>
> > -----------------<br>
> > grompp.mdp<br>
> > title = ThreeAtoms<br>
> > integrator = md<br>
> > dt = 0.001<br>
> > nsteps = 1<br>
> > ns_type = grid<br>
> > pbc = xyz<br>
> > coulombtype = shift<br>
> > rlist = 1.4<br>
> > rcoulomb = 1.4<br>
> > rvdw = 1.4<br>
> > tcoupl = no<br>
> > pcoupl = no<br>
> > constraint_algorithm = shake<br>
> > shake_tol = 1e-4<br>
> > gen-vel = no<br>
> > gen-temp = 0<br>
> ><br>
> > nstxout = 1<br>
> > nstvout = 0<br>
> > nstfout = 0<br>
> ><br>
> > pull = umbrella<br>
> > pull_geometry = distance<br>
> > pull_dim = N N Y<br>
> > pull_start = no<br>
> > pull_init1 = 0.7<br>
> > pull_group0 = Ref<br>
> > pull_group1 = Pulled<br>
> > pull_k1 = 10000<br>
> > -----------------<br>
> > topology.top<br>
> > ; topology for two partially charged atoms<br>
> ><br>
> > [ defaults ]<br>
> > ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ<br>
> > 1 3 yes 0.125 0.5<br>
> ><br>
> > [ atomtypes ]<br>
> > ;name mass charge ptype sig eps<br>
> > A 1000.0000 0.000 A 0.50000 9.90000<br>
> > B 9.0000 0.000 A 0.30000 9.00000<br>
> ><br>
> > [ nonbond_params ]<br>
> > ; i j func sig eps<br>
> ><br>
> > [ moleculetype ]<br>
> > AAAA 1<br>
> ><br>
> > [ atoms ]<br>
> > ; nr type resnr residue atom cgnr charge mass<br>
> > 1 A 1 AAA A 1 0.000 1000.0000<br>
> ><br>
> > [ moleculetype ]<br>
> > BBBB 1<br>
> ><br>
> > [ atoms ]<br>
> > ; nr type resnr residue atom cgnr charge mass<br>
> > 1 B 1 BBB B 1 0.000 9.00<br>
> ><br>
> > [ system ]<br>
> > ; name<br>
> > Three atoms<br>
> ><br>
> > [ molecules ]<br>
> > ; name number<br>
> > AAAA 2<br>
> > BBBB 1<br>
> ><br>
> ><br>
> ><br>
> ><br>
> ><br>
> > Chris Neale wrote:<br>
> >> I just checked similar simulations of mine and Berk's
suggestion <br>
> >> accounts for similar discrepancies that I notice on a
quick <br>
> >> evaluation where g_traj and g_dist fail to give me the
same distance <br>
> >> as I obtain from the pull pos.xvg file. As Berk suggests,
once I <br>
> >> first trjconv -center -pbc mol -ur compact (giving an
appropriate <br>
> >> residue for centering that puts all relevant pulled atoms
in the same <br>
> >> box) then g_traj and g_dist both give me the exact same
answer as I <br>
> >> calculate based on pull pos.xvg. Chris -- original
message -- Hi, <br>
> >> There could be a problem with periodic boundary
conditions. Do you <br>
> >> have multiple molecules in a pull group, or broken
molecules? In that <br>
> >> case the COM position of 3.3.3 and g_traj are both
incorrect. The <br>
> >> pull code in 4.0 grompp and mdrun are (as far as I know)
always <br>
> >> correct. Berk<br>
> ><br>
> > _______________________________________________<br>
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> ><br>
> ><br>
> <br>
> <br>
> -- <br>
> Steve Fiedler, Ph.D.<br>
> Research Fellow<br>
> Department of Mechanical Engineering<br>
> The University of Michigan<br>
> 2024 G.G. Brown<br>
> 2350 Hayward St.<br>
> Ann Arbor, MI 48109-2125<br>
> <br>
> <br>
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