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Dear Gromacs users,<br>
<br>
In continuation to the problem below, it seems that self interaction is
not the problem since a -d 1.5nm around the protein should have been
more than enough. Not noticing earlier, I see strange files being
created with the name "step1150b_n1.pdb"<br>
(a bug like structural report of that step ?). In those files and in
the pdb created after applying trjconv, the protein is drifted from the
cell's center to one of the edge and a fragment appears at the other
side.<br>
Saying that, trjconv does not solves the problem.<br>
<br>
I would be most thankful for any comment/suggestion as to how to
prevent this drift which causes in turn to the "fragment" problem.<br>
<br>
Thank<br>
<br>
Arik<br>
<br>
Mark James Abraham wrote:
<blockquote cite="mid:7400a37f3a98.4b3df775@anu.edu.au" type="cite">
<div style="font-size: 16px; font-family: 'times new roman';">
<div><br>
</div>
<div>On 01/01/10, <b class="name">"Justin A. Lemkul" </b><a class="moz-txt-link-rfc2396E" href="mailto:jalemkul@vt.edu"><jalemkul@vt.edu></a>
wrote:</div>
<blockquote cite="mid:4B3D1E21.8090601@vt.edu" class="iwcQuote"
style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0px;"
type="cite"><br>
<br>
Arik Cohen wrote:<br>
>No, sorry for the confusion. The images are only from a simulation
of one protein(tmRBP_Unliganded, PDB: 2FN9). The problem seen with BPTI
was a bit different in a way that only 1 C-alpha was "detached" (cell
size ?).<br>
><br>
<br>
If there is supposed to be only a single protein in the images you've
shown (and after having a look at the 2FN9 structure from the PDB), it
seems pretty clear to me that part of your protein has simply crossed a
periodic boundary and trjconv -pbc mol (or some such command) should
fix it.<br>
</blockquote>
<div>Indeed. Further, note that the reappearance of a subset of the
seemingly detached atoms back with the main group is totally normal.
With domain decomposition in GROMACS 4, such "broken" molecules can be
written to the trajectory. Judicious use of trjconv fixes the
appearance of this non-problem.</div>
<div><br>
</div>
<div>Mark</div>
<div><br>
</div>
<blockquote cite="mid:4B3D1E21.8090601@vt.edu" class="iwcQuote"
style="border-left: 1px solid rgb(0, 0, 255); padding-left: 13px; margin-left: 0px;"
type="cite">
<div class="mimepart text plain"><br>
>Arik<br>
><br>
>Justin A. Lemkul wrote:<br>
>><br>
>><br>
>>Arik Cohen wrote:<br>
>>>Which two proteins ? I have at least in beginning only one
protein which some how is divided into two along the calculation.<br>
>>>Any way I'll try both increasing the cell and fix it with
trjconv.<br>
>>><br>
>><br>
>>Quoting your original message:<br>
>><br>
>>"While running a simple MD simulation with both a small protein
such as BPTI and a larger one such as tmRBP_Unliganded_2FN9.pdb..."<br>
>><br>
>>I assumed that what I was seeing in the images was a set of two
proteins. My concern was that you defined a box relative to the larger
protein, then inserted the smaller one (BPTI?), leaving insufficient
space in the box to satisfy the minimum image convention. If that's
not what we're looking at, then that'd be useful to know :)<br>
>><br>
>>If you have a single protein, "divided into two" then the
problem is almost certainly a simple periodicity artifact. Bonds do
not break in a normal MD calculation (in fact they can't using the
standard MM approximations).<br>
>><br>
>>-Justin<br>
>><br>
>>>Thanks a lot<br>
>>><br>
>>>Arik<br>
>>><br>
>>>Justin A. Lemkul wrote:<br>
>>>><br>
>>>><br>
>>>>Arik Cohen wrote:<br>
>>>>>I'm using dodecahedron -d 0.7<br>
>>>>><br>
>>>>><br>
>>>><br>
>>>>Was that distance specified with respect to both of the
protein molecules in the unit cell? You can check for spurious PBC
interactions with g_mindist -pi. Anyway, I'd be curious to see how you
do with trjconv.<br>
>>>><br>
>>>>-Justin<br>
>>>><br>
>>>>><br>
>>>>>Justin A. Lemkul wrote:<br>
>>>>>><br>
>>>>>><br>
>>>>>>Arik Cohen wrote:<br>
>>>>>>>Hi,<br>
>>>>>>><br>
>>>>>>>I have not tried yet to fix it with trjconv
which I will . Attached is a picture with 4 snapshots taken from the
simulation. The C-alphas in question are emphasized with red color.<br>
>>>>>>><br>
>>>>>><br>
>>>>>>Is your unit cell sufficiently large? It looks
like the C-alphas indicated are simply crossing the periodic boundary
on the "left" of the frame and interacting with the protein molecule in
the "right" of the frame, which would indicate to me that the unit cell
is too small and you're seeing spurious PBC interactions (i.e.,
violation of the minimum image convention).<br>
>>>>>><br>
>>>>>>-Justin<br>
>>>>>><br>
>>>>>>>Thanks<br>
>>>>>>><br>
>>>>>>>Arik<br>
>>>>>>><br>
>>>>>>>Justin A. Lemkul wrote:<br>
>>>>>>>><br>
>>>>>>>><br>
>>>>>>>>Arik Cohen wrote:<br>
>>>>>>>>>Hi,<br>
>>>>>>>>><br>
>>>>>>>>>Sorry to bother you again ,but its
not only a periodic effect since only *some of the atoms* in the
"Detached" group are vanishing from this group and reappearing in the
main protein group. The rest of the atoms are either always in the
detached or the main group.<br>
>>>>>>>>>In addition, the "detached" group
includes three segments of the protein(8 residues(126-131), 8
residues(157-164) and 4 residues186-189).<br>
>>>>>>>>><br>
>>>>>>>><br>
>>>>>>>>From your description, this sounds
exactly like a periodicity problem - some of the atoms are crossing the
periodic boundary and are appearing in strange locations. Have you
even tried trjconv to fix it? That would be useful information, as I
see that Mark long ago also suggested the same sort of fix.<br>
>>>>>>>><br>
>>>>>>>>It is hard for me to envision what you
are seeing. It would be enormously helpful if you could post images
(screenshots, etc) of the problematic structures to get a more
expedient resolution.<br>
>>>>>>>><br>
>>>>>>>>-Justin<br>
>>>>>>>><br>
>>>>>>>>>Thanks a lot<br>
>>>>>>>>><br>
>>>>>>>>>Arik<br>
>>>>>>>>><br>
>>>>>>>>>Justin A. Lemkul wrote:<br>
>>>>>>>>>><br>
>>>>>>>>>><br>
>>>>>>>>>>Arik Cohen wrote:<br>
>>>>>>>>>>>Hi,<br>
>>>>>>>>>>><br>
>>>>>>>>>>>With regards to your
question I do see some periodicity in which for a section of time in
the trajectory some of the Calphas in the "detached group" are
vanishing from it and reappear in the main protein.<br>
>>>>>>>>>>>In addition,<br>
>>>>>>>>>>>I would appreciate as
before any suggestion you might have in the matter.<br>
>>>>>>>>>>><br>
>>>>>>>>>><br>
>>>>>>>>>>If this is just a periodicity
artifact, fix it with trjconv.<br>
>>>>>>>>>><br>
>>>>>>>>>>-Justin<br>
>>>>>>>>>><br>
>>>>>>>>>>>Thanks<br>
>>>>>>>>>>><br>
>>>>>>>>>>>Arik<br>
>>>>>>>>>>><br>
>>>>>>>>>>>Mark Abraham wrote:<br>
>>>>>>>>>>>>Arik Cohen wrote:<br>
>>>>>>>>>>>>>Hi,<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>>Thanks for
answering so quickly !. Apparently whole residues have detached from
the protein.<br>
>>>>>>>>>>>><br>
>>>>>>>>>>>>So... like I asked last
time, are you seeing a periodicity artefact? "Detached" covers a whole
gamut of possibilities.<br>
>>>>>>>>>>>><br>
>>>>>>>>>>>>>Another strange
thing that happens in pyMol and VMD is that when I select an atom or a
residue in the detached group the selection appears twice: one in the
detached group and one in the main part.<br>
>>>>>>>>>>>><br>
>>>>>>>>>>>>If you've got atoms
duplicated, then it sounds like something's going wrong with how
they're interpreting the structure file, or how you're manipulating it
afterwards. Either way, it's not a problem for the GROMACS mailing list
unless you can demonstrate the atoms are duplicated in the structure
file (which they aren't!).<br>
>>>>>>>>>>>><br>
>>>>>>>>>>>>Mark<br>
>>>>>>>>>>>><br>
>>>>>>>>>>>>>Arik<br>
>>>>>>>>>>>>><br>
>>>>>>>>>>>>>Mark Abraham wrote:<br>
>>>>>>>>>>>>>>Arik Cohen
wrote:<br>
>>>>>>>>>>>>>>>Dear
GROMACS users,<br>
>>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>>While
running a simple MD simulation with both a small protein such as BPTI
and a larger one such as tmRBP_Unliganded_2FN9.pdb, I'm encountering an
odd situation in which one (in the case of BPTI) or several Calphas (in
the later case) are "detaching them selfs" from the main group.<br>
>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>"main group" of
what? Do the atoms bound to them move also? Are you seeing a
periodicity artefact?<br>
>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>Mark<br>
>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>>The problem
appeared only after adding salt to the simulation(at least in the case
of BPTI).<br>
>>>>>>>>>>>>>>>I would
appreciate any suggestions and comments on the matter.<br>
>>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>>Thanks<br>
>>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>>Arik<br>
>>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>>The run
files are:<br>
>>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>>*em.mdp:*<br>
>>>>>>>>>>>>>>>
title = tmRBP_Unliganded_2FN9 Minimization<br>
>>>>>>>>>>>>>>>integrator
= steep ; (steep)using steepest descent<br>
>>>>>>>>>>>>>>>nsteps
= 50000<br>
>>>>>>>>>>>>>>>nstlist
= 1<br>
>>>>>>>>>>>>>>>rlist
= 1.0<br>
>>>>>>>>>>>>>>>coulombtype
= PME<br>
>>>>>>>>>>>>>>>rcoulomb
= 1.0<br>
>>>>>>>>>>>>>>>vdw-type
= cut-off<br>
>>>>>>>>>>>>>>>rvdw
= 1.0<br>
>>>>>>>>>>>>>>>nstenergy
= 10<br>
>>>>>>>>>>>>>>>emtol
= 5.0 ; tolerance kJ/(Mol -1 nm-1) instead of 10.0<br>
>>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>>*pr.mdp<br>
>>>>>>>>>>>>>>>*<br>
>>>>>>>>>>>>>>>title
= tmRBP_Unliganded_2FN9 PR<br>
>>>>>>>>>>>>>>>integrator
= md<br>
>>>>>>>>>>>>>>>nsteps
= 50000<br>
>>>>>>>>>>>>>>>dt
= 0.002 ;(in ps) doing a 100ps traj.<br>
>>>>>>>>>>>>>>>constraints
= all-bonds<br>
>>>>>>>>>>>>>>>nstlist
= 10 ; neighbour list updates every number of steps<br>
>>>>>>>>>>>>>>>rlist
= 1.0<br>
>>>>>>>>>>>>>>>coulombtype
= PME<br>
>>>>>>>>>>>>>>>rcoulomb
= 1.0<br>
>>>>>>>>>>>>>>>vdw-type
= cut-off<br>
>>>>>>>>>>>>>>>rvdw
= 1.0<br>
>>>>>>>>>>>>>>>tcoupl
= Berendsen<br>
>>>>>>>>>>>>>>>tc-grps
= Protein non-protein<br>
>>>>>>>>>>>>>>>tau-t
= 0.1 0.1<br>
>>>>>>>>>>>>>>>ref-t
= 298 298<br>
>>>>>>>>>>>>>>>Pcoupl
= Berendsen<br>
>>>>>>>>>>>>>>>tau-p
= 1.0<br>
>>>>>>>>>>>>>>>compressibility
= 5e-5 5e-5 5e-5 0 0 0<br>
>>>>>>>>>>>>>>>ref-p
= 1.0<br>
>>>>>>>>>>>>>>>nstenergy
= 100<br>
>>>>>>>>>>>>>>>define
= -DPOSRES ; include posre.itp(position restraint) file<br>
>>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>>*run.md<br>
>>>>>>>>>>>>>>>*title
= tmRBP_Unliganded_2FN9<br>
>>>>>>>>>>>>>>>integrator
= md<br>
>>>>>>>>>>>>>>>nsteps
= 300000<br>
>>>>>>>>>>>>>>>dt
= 0.001<br>
>>>>>>>>>>>>>>>constraints
= all-bonds<br>
>>>>>>>>>>>>>>>nstlist
= 10<br>
>>>>>>>>>>>>>>>rlist
= 1.0<br>
>>>>>>>>>>>>>>>coulombtype
= PME<br>
>>>>>>>>>>>>>>>rcoulomb
= 1.0<br>
>>>>>>>>>>>>>>>vdw-type
= cut-off<br>
>>>>>>>>>>>>>>>rvdw
= 1.0<br>
>>>>>>>>>>>>>>>tcoupl
= V-rescale ;V-rescale<br>
>>>>>>>>>>>>>>>tc-grps
= Protein non-protein<br>
>>>>>>>>>>>>>>>tau-t
= 0.8 0.8<br>
>>>>>>>>>>>>>>>ref-t
= 298 298<br>
>>>>>>>>>>>>>>>nstxout
= 1000<br>
>>>>>>>>>>>>>>>nstvout
= 1000<br>
>>>>>>>>>>>>>>>nstxtcout
= 1000<br>
>>>>>>>>>>>>>>>nstenergy
= 1000<br>
>>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>>The runs
commands are(integrated inside a C++ code):<br>
>>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>>SysCommand1
= "echo 6 | pdb2gmx -f " + FileName + " -water tip3p";<br>
>>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>>
system("editconf -f conf.gro -bt dodecahedron -d 0.7 -o box.gro");<br>
>>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>>system("genbox
-cp box.gro -cs spc216.gro -p topol.top -o solvated.gro");<br>
>>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>>minimization:<br>
>>>>>>>>>>>>>>>--------<br>
>>>>>>>>>>>>>>> if(Mode ==
"NoSalt")<br>
>>>>>>>>>>>>>>> {<br>
>>>>>>>>>>>>>>>
system("grompp -f MDP/em.mdp -p topol.top -c solvated.gro -o em.tpr");<br>
>>>>>>>>>>>>>>>
//system("mpirun -np 4 mdrun -v -deffnm em");<br>
>>>>>>>>>>>>>>> }<br>
>>>>>>>>>>>>>>> if(Mode
== "WithSalt")<br>
>>>>>>>>>>>>>>> {<br>
>>>>>>>>>>>>>>>
system("grompp -f MDP/em.mdp -p topol.top -c solvated.gro -o em.tpr");<br>
>>>>>>>>>>>>>>>
system("mpirun -np 4 mdrun -v -deffnm em");<br>
>>>>>>>>>>>>>>> }<br>
>>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>><br>
>>>>>>>>>>>>>>>Salting:<br>
>>>>>>>>>>>>>>>--------<br>
>>>>>>>>>>>>>>>
system("echo 12 | genion -s em.tpr -conc 0.1 -neutral -o solvated.gro");<br>
>>>>>>>>>>>>>>> pr:<br>
>>>>>>>>>>>>>>>----<br>
>>>>>>>>>>>>>>>system("grompp
-f MDP/prmd.mdp -p topol.top -c em.gro -o pr.tpr");<br>
>>>>>>>>>>>>>>> /* The
actual run*/<br>
>>>>>>>>>>>>>>>
system("mpirun -np 4 mdrun -v -deffnm pr"); <br>
>>>>>>>>>>>>><br>
>>>>>>>>>><br>
>>>>>>>><br>
>>>>>>><br>
>>>>>>>------------------------------------------------------------------------
<br>
>>>>>>><br>
>>>>>><br>
>>>>><br>
>>>><br>
>>><br>
>><br>
><br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]vt.edu | (540) 231-9080<br>
<a moz-do-not-send="true" _zipidx="1001"
href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin"
target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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</blockquote>
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