[gmx-users] Problem in energy minimization for a empty membrane system
Justin A. Lemkul
jalemkul at vt.edu
Wed Jun 24 14:14:42 CEST 2009
Bing Bing wrote:
> Hi!
> Thanks for your suggestion on the tutorial. I will try it out.
> I actually tried to use the starting structure without going through
> editconf and alteration but it failed. Here's the error:
> ERROR: The cut-off length is longer than half the shortest box vector or
> longer than the smallest box diagonal element. Increase the box size or
> decrease rlist.
> I've tried on reducing the rlist but still failed. Please advice.
>
The POPC bilayer from Tieleman's site is a 6.2 x 6.1 nm box in x-y, and 6.9 nm
in z. How large are your cutoffs? You do realize that Gromacs uses nm, not
Angstrom, for these parameters, right?
> According to the tutorial you suggested, we are suppose to use genbox to
> solvate the membrane and remove those water manually by script that go
> inside the membrane. Does this mean that I'm suppose to throw away the
> water from the starting structure and resolvate it again?
>
I pointed you to the tutorial because you said you'd be running a membrane
protein. For a pure membrane, you do not need to remove water and re-solvate.
The POPC structure Tieleman provides is pre-equilibrated, so it should be fine
for a simulation of just the membrane.
-Justin
> thanks again.
>
> regards,
> Bing
>
> On Tue, Jun 23, 2009 at 11:28 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> Bing Bing wrote:
>
> Thanks for reply.
> I've used editconf to define the box by issuing :-
> editconf -f popc.pdb -o popc_box.gro -c -d 1.0 -bt cubic
> Is this the correct way of using editconf?
>
>
> This would be appropriate for a protein, but not a membrane. What
> you're doing is defining a layer of nothingness around the
> membrane/water system, which may have molecules split across
> periodic boundaries. This could be the reason everything is blowing up.
>
> Try running EM on the original, unaltered POPC from Tieleman's site.
>
>
> And with this i proceed with grompp with the mdp file from
> previous email followed by mdrun....
>
> Actually the restraint is require in another system
> (membrane+protein), i wanted to test it out in the this smaller
> systme before using it in the complete systme.However, it failed.
>
>
> Applying position restraints to every atom of a lipid in the
> presence of a protein still serves little purpose. If you were to
> attempt to energy-minimize such a system, the clashes (if any)
> between the protein and lipids would go unresolved. Certainly
> equilibrating with such restraints would be meaningless, as well.
>
> If you're interested, hopefully the tutorial here will help:
>
> http://oldwiki.gromacs.org/index.php/Membrane_Simulations
>
> It is designed for membrane protein simulations.
>
> -Justin
>
> Thanks in advance
>
> regards,
> bing
>
>
> On Tue, Jun 23, 2009 at 10:21 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>
>
>
> Bing Bing wrote:
>
> Hi Justin,
> I've tried with no restraint and the minimization stopped
> at the
> same time. I actually suspect that the restraint is not
> working
> at all. My top file is as below:-
> #include "ffG53a6_lipid.itp"
> #include "popc.itp"
> #ifdef POSRES
> #include "posres_popc.itp"
> #endif
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
>
> [ system ]
> ; name
> Pure POPC bilayer with 128 lipids 2460 water
>
> [ molecules ]
> ; name number
> POPC 128
> SOL 2460
>
> my posres_popc.itp is as below:-
> [ position_restraints ]
> ; atom type fx fy fz
> 1 1 1000 1000 1000
> .....
> 51 1 1000 1000 1000
> 52 1 1000 1000 1000
>
> my mdp file as below :-
> define = -DPOSRES
> integrator = steep
> emtol = 1000
> emstep = 0.01
> nsteps = 100
> rlist = 1.2
> coulombtype = PME
> rcoulomb = 1.2
> rvdw = 1.2
> constraints = none
>
> May i know that is the top, posres and also the mdp file
> correctly done?
>
>
> Well, they are syntactically correct, it seems. I see no
> purpose in
> restraining lipids during a minimization, however.
>
>
> And by looking at the log file in the previous mail, is it
> confirm that it manage to read the restraint file?
>
>
> Can't tell. Your system is crashing instantly for some reason.
>
>
> The starting structure is taken from Peter Tielemen
> website and
> what i did is editconf to make box and i didn't solvate
> because
> the starting structure come together with water. I'm not sure
> this is the correct way of doing it. Please advice.
>
>
> Please define "editconf to make box" - have you somehow
> manipulated
> the structure? That could be a source of error. The
> structure that
> Tieleman provides minimized for me with no problem when I used it
> recently.
>
> -Justin
>
>
>
> Thanks in advance.
> Bing
>
>
>
> On Tue, Jun 23, 2009 at 7:16 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>>> wrote:
>
>
>
> Bing Bing wrote:
>
> Hi! I'm a postgraduate student from Malaysia and
> currently
> facing energy minimization problem for my membrane
> system.
> I'm trying to perform energy minimization for an
> empty POPC
> membrane with position restraint on the lipid.
> Minimization stop
> due to inf Fmax. And I noticed that in the log file as
> below:-
> Initiating Steepest Descents
> Max number of connections per atom is 25
> Total number of connections is 84976
> Max number of graph edges per atom is 4
> Total number of graph edges is 22896
> Going to use C-settle (2460 waters)
> wo = 0.333333, wh =0.333333, wohh = 3, rc =
> 0.08165, ra =
> 0.0384897
> rb = 0.0192448, rc2 = 0.1633, rone = 1, dHH =
> 0.1633, dOH
> = 0.1
> Started Steepest Descents on node 0 Tue Jun 23
> 17:03:43 2009
> Steepest Descents:
> Tolerance (Fmax) = 1.00000e+03
> Number of steps = 100
> Grid: 11 x 11 x 11 cells
> Step Time Lambda
> 0 0.00000 0.00000
> Energies (kJ/mol)
> Bond Angle Proper Dih.
> Ryckaert-Bell.
> Improper Dih.
> 1.64082e+05 1.71875e+04 4.06560e+03
> 6.45104e+03 8.36392e+03
> LJ-14 Coulomb-14 LJ (SR) Coulomb
> (SR) Coul. recip.
> 2.12067e-314 2.12067e-314 -1.58963e+04
> -1.05392e+05 -1.15292e+05
> Position Rest. Potential Pressure (bar)
> 0.00000e+00 -3.64297e+04 nan
>
>
> >From the looks of some of these energies (i.e., LJ-14,
> Coulomb-14), it looks like something is severely wrong
> with your
> starting structure, and applying position restraints
> probably
> isn't
> helping.
>
> Try the minimization without restraints and see if it
> works.
>
> Also, have you set the appropriate "define" line in
> the .mdp
> file,
> corresponding to what is prescribed in the .top?
>
> -Justin
>
>
> -------------------------------------------------------
> Program mdrun_d, VERSION 4.0.5
> Source code file: nsgrid.c, line: 357
> Range checking error:
> Explanation: During neighborsearching, we assign each
> particle
> to a grid
> based on its coordinates. If your system contains
> collisions or
> parameter
> errors that give particles very high velocities
> you might
> end up
> with some
> coordinates being +-Infinity or NaN (not-a-number).
> Obviously,
> we cannot
> put these on a grid, so this is usually where we
> detect those
> errors.
> Make sure your system is properly energy-minimized and
> that the
> potential
> energy seems reasonable before trying again.
> Variable ci has value -2147483648. It should have been
> within [
> 0 .. 1331 ]
> the position restraint energy is 0 as highlighted.
> Here's the
> position restraint file :-
> [ position_restraints ]
> ; atom type fx fy fz
> 1 1 1000 1000 5000
> 5 1 1000 1000 1000
> 6 1 1000 1000 1000
> 7 1 1000 1000 1000
> 8 1 1000 1000 1000
> 9 1 1000 1000 1000
> 10 1 1000 1000 1000
> ......
>
> whereby the restraint energy is 1000kcal/mol in x,
> y and z
> plane. In the log file the position restraint
> energy is
> stated
> as 0.0000e+00 (as highlighted above).
> I think that the position restraint is not working
> fine
> here. Is
> there anyways to solve this? did I miss out
> something here?
> I would be grateful if anyone can advice me on this.
>
> ------------------------------------------------------------------------
>
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> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu>
> <http://vt.edu> | (540)
>
> 231-9080
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> -- ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
> 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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