[gmx-users] Problem in energy minimization for a empty membrane system

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 23 16:21:04 CEST 2009



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>> 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> | (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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