[gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance
Steve Fiedler
fiedler at umich.edu
Mon Jan 26 23:46:26 CET 2009
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
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use thewww
> interface or send it to gmx-users-request at gromacs.org.
> 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
More information about the gromacs.org_gmx-users
mailing list