[gmx-users] L-BFGS energy minimization wrong!

[Stéphane Téletchéa]

zzhwise1 a écrit :
> hi everyone !
>    i have ask some questions about energy minimization before ,but 
> still,there are problems !this time it show:
> -------------------------------------------------------                    
> Program mdrun, VERSION 3.3.1                                               
> Source code file: nsgrid.c, line: 226                                      
>                                                                            
> 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 .. 250 ] 
> Please report this to the mailing list (gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>)             
> -------------------------------------------------------                    
>                                                                            
> and my gro has no problem!my mdp is :
> title               = lbfilm, 300K                
> cpp                 =  /bin/cpp                   
> define              =                             
> constraints         =  none                       
> integrator          =  l-bfgs                     
> ;dt                  =  0.002 ; ps !              
> nsteps              =  5000 ; total 60 ns.        
> nstlog              =  1                          
> nstenergy           =  1                          
> emtol               =  10.0                       
> emstep              =  0.01                       
> ;nstcgsteep          =  10                        
> niter               =  20                         
> nbfgscorr           =  10                         
> nstlist             =  1                          
> ns_type             =  grid                       
> pbc                 =  xyz                        
> coulombtype         =  PME                        
> rlist               =  1.1                        
> rcoulomb            =  1.1                        
> vdwtype             = switch                      
> rvdw-switch         = 0.9                         
> rvdw                = 1.0                         
> Dispcorr            = EnerPres                    
>                                                   
> my system is two parell monolayes  and the distance is 1.5 nm !
> could any one give me any advice?
> thanks!
>  

Hi,

I would avoid the switch function for calculating Van Der Wall
interactions since it seems not appropriate (see Van Der Spoel and van
Maaren, JCTC, 2006, 2, 1-11).

Try using regular vdw radius of 1.4 nm.

I would use:

coulombtype         =  PME
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  1.4


Cheers,

Stéphane

-- 
Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901