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

[Justin A. Lemkul]

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.
>  
>  
>  
> 
>  
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.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 the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-- 
========================================

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

========================================