AMBER Archive (2004)

Subject: AMBER: Vlimit problem

From: Yuqin Cai (yc385_at_nyu.edu)
Date: Thu Jan 08 2004 - 12:15:38 CST

 

Dear Amber users,

I have encountered a problem with vlimit when runing the simulation of an unmodified control of a 11mer B - DNA with 20 Na+ counterions added and  waterbox of 10 A in each dimension. I set vlimit=15.0 for the second step "dynamics holding the solute fixed",after 1000 steps of steepest descent minimization and 4000 steps of conjugate gradient minimization.  The output file indicates that vlimit is exceeded. I follow the example form  the tutorial. How is the value in the example shown in the tutorial chosen? Can I possibly enlarge the vlimit to 20.O?  Attached are the output files. Any suggestions?

And another question, is it possible to change the random number seed card "IG" to get a better results ? If so what's the algorithm to get other random numbers ? And should I keep the same IG for the whole run of dynamics ?

thanks a lot,

yuqin

Here is the input file:

5DNB, initial dynamics w/ belly on DNA, model1, 9.0 cut                       
&cntrl                                                                       
                                                                              
  nmropt = 1,                                                                 
  ntx    = 1,       irest  = 0,       ntrx   = 1,      ntxo   = 1,            
  ntpr   = 100,     ntwx   = 500,     ntwv   = 0,      ntwe   = 0,            
                                                                              
  ntf    = 2,       ntb    = 2,                                               
  cut    = 9.0,     nsnb   = 10,                                              
                                                                              
  ibelly = 0,       ntr    = 1,                                               
                                                                              
  imin   = 0,                                                                 
  nstlim = 12500,                                                             
  nscm   = 500,                                                               
  t      = 0.0,     dt     = 0.002,                                           
                                                                              
  temp0  = 300.0,   tempi  = 10.0,                                            
  ig     = 10000,   heat   = 0.0,                                             
  ntt    = 1,                                                                 
  tautp  = 1.0,                                                               
  vlimit = 15.0,                                                              
                                                                              
  ntp    = 1,       pres0  = 1.0,     comp   = 44.6,                          
  taup   = 1.0,     npscal = 1,                                               
                                                                              
  ntc    = 2,       tol    = 0.000001,                                        
                                                                              
&end                                                                         
&wt                                                                          
   type='TEMP0', istep1=0,     istep2=10000,                                  
                 value1=10.0,  value2=300.0,                                  
&end                                                                         
&wt                                                                          
   type='TEMP0', istep1=10001,   istep2=12500,                                
                 value1=300.0, value2=300.0,                                  
&end                                                                         
&wt                                                                          
   type='END',                                                                
&end                                                                         
&rst                                                                         
   iat=0,                                                                     
&end                                                                         
Hold the DNA fixed                                                            
500.0                                                                         
RES  1  22                                                                    
END                                                                           
END                                                                            
4.  RESULTS
--------------------------------------------------------------------------------

---------------------------------------------------
APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
using   5000.0 points per unit in tabled values
TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err =   0.2088E-14   at   2.598900
| CHECK d/dx switch(x): max rel err =   0.7671E-11   at   2.757160
---------------------------------------------------
| Local SIZE OF NONBOND LIST =     637655
| TOTAL SIZE OF NONBOND LIST =    2446227

NSTEP =      0 TIME(PS) =     0.000  TEMP(K) =    14.85  PRESS = -5099.7
Etot   =  -49003.6423  EKtot   =     354.2138  EPtot      =  -49357.8561
BOND   =      30.2168  ANGLE   =     467.1109  DIHED      =     471.4457
1-4 NB =     260.6332  1-4 EEL =   -2725.1540  VDWAALS    =    7150.9579
EELEC  =  -55312.5627  EHBOND  =       0.0000  RESTRAINT  =     299.4961
EAMBER (non-restraint)  =  -49657.3521
EKCMT  =     110.6791  VIRIAL  =   18210.9482  VOLUME     =  164384.1067
                                                Density    =       0.7427
Ewald error estimate:   0.1204E-03
------------------------------------------------------------------------------

===============================================================================
                      NMR restraints for step      0
Energy (this step): Bond =    0.000   Angle =     0.000   Torsion =     0.000
Energy (tot. run) : Bond =    0.000   Angle =     0.000   Torsion =     0.000

DEVIATIONS:    Target=(r2+r3)/2                 Target = closer of r2/r3
            This step         Entire run        This step        Entire run
           ave.    rms       ave.    rms       ave.    rms      ave.     rms
Bond      0.000   0.000     0.000   0.000     0.000   0.000     0.000   0.000
Angle     0.000   0.000     0.000   0.000     0.000   0.000     0.000   0.000
Torsion   0.000   0.000     0.000   0.000     0.000   0.000     0.000   0.000
===============================================================================
vlimit exceeded for step            2; vmax =    17.13467864910667   
vlimit exceeded for step            3; vmax =    16.46050656840751   
vlimit exceeded for step            4; vmax =    15.33594357993587   
vlimit exceeded for step           13; vmax =    15.70078550834117   
vlimit exceeded for step           14; vmax =    16.59991220287259   
vlimit exceeded for step           15; vmax =    16.86371180947484   
vlimit exceeded for step           16; vmax =    16.57031937054190   
vlimit exceeded for step           17; vmax =    16.34291035410589   
vlimit exceeded for step           18; vmax =    15.70844755064599   
vlimit exceeded for step           28; vmax =    15.56435966114940   
vlimit exceeded for step           29; vmax =    16.06470690834402   
vlimit exceeded for step           30; vmax =    16.10820900045790   
vlimit exceeded for step           31; vmax =    16.17361514145253    
                   

                                                

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