md3.out

          -------------------------------------------------------
          Amber 12 SANDER                              2012
          -------------------------------------------------------

| PMEMD implementation of SANDER, Release 12

| Run on 02/19/2015 at 01:02:22

  [-O]verwriting output

File Assignments:
|   MDIN: mdshort.in                                                            
|  MDOUT: md3.out                                                               
| INPCRD: md3.crd                                                               
|   PARM: penta.top                                                             
| RESTRT: md3.rst                                                               
|   REFC: refc                                                                  
|  MDVEL: mdvel                                                                 
|   MDEN: mden                                                                  
|  MDCRD: md3.ncdf                                                              
| MDINFO: md3.inf                                                               
|LOGFILE: logfile                                                               

 
 Here is the input file:
 
0.1 ns GBSA sim of pentapeptide                                                
 &cntrl                                                                        
   imin=0, ntx=1,                                                              
   ntpr=1000, ntwr=1000, ntwx=500,                                             
   ioutfm=1,                                                                   
   nstlim=50000, dt=0.002,                                                     
   ntt=3, ig=-1, gamma_ln=5.0,                                                 
   ntc=2, ntf=2,                                                               
   ntb=0, cut=25.0, igb=2,                                                     
 &end                                                                          


Note: ig = -1. Setting random seed based on wallclock time in microseconds
      and disabling the synchronization of random numbers between tasks
      to improve performance.
 
| ERROR:   I could not understand line     3
************************************************************************        

*s in the inpcrd file often indicate an overflow of the Fortran format used
to store coordinates in the inpcrd/restart files. This often happens when
particles diffuse very far away from each other. Make sure you are removing
center-of-mass translation (nscm /= 0) or check if you have multiple, mobile
molecules that have diffused very far away from each other. This condition is
highly unusual for non-periodic simulations.