[gmx-users] NPT for compressing

Justin A. Lemkul jalemkul at vt.edu
Sun May 22 04:30:08 CEST 2011



Elisabeth wrote:
> 
> 
> On 21 May 2011 19:02, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     Elisabeth wrote:
> 
> 
> 
> 
> 
>         On 20 May 2011 23:04, Mark Abraham <Mark.Abraham at anu.edu.au
>         <mailto:Mark.Abraham at anu.edu.au> <mailto:Mark.Abraham at anu.edu.au
>         <mailto:Mark.Abraham at anu.edu.au>>> wrote:
> 
>            On 21/05/2011 10:45 AM, Elisabeth wrote:
> 
>                Dear  experts,
> 
>                I have a box of pure hexane with density of around 50 SI
>             (size
>                7nm). With the settings below I get error:
> 
>                vol 0.65  imb F  3% step 42100, will finish Fri May 20
>             18:54:05 2011
>                Warning: 1-4 interaction between 1246 and 1249 at
>             distance 3.580
>                which is larger than the 1-4 table size 2.250 nm
>                These are ignored for the rest of the simulation
>                This usually means your system is exploding,
>                if not, you should increase table-extension in your mdp file
>                or with user tables increase the table size
>                Warning: 1-4 interaction between 1249 and 1252 at
>             distance 3.693
>                which is larger than the 1-4 table size 2.250 nm
>                These are ignored for the rest of the simulation
>                This usually means your system is exploding,
>                if not, you should increase table-extension in your mdp file
>                or with user tables increase the table size
> 
>                A list of missing interactions:
>                                Bond of   2375 missing      2
>                               Angle of   4500 missing     11
>                      Ryckaert-Bell. of   5625 missing     21
>                               LJ-14 of   5625 missing     15
> 
>                Molecule type 'Hexane'
>                the first 10 missing interactions, except for exclusions:
>                      Ryckaert-Bell. atoms    5    8   11   14 global
>              1245  1248     1251  1254
>                               LJ-14 atoms    5   14           global
>              1245  1254
>                               Angle atoms    8   11   14      global
>              1248  1251     1254
>                      Ryckaert-Bell. atoms    8   11   14   15 global
>              1248  1251     1254  1255
>                      Ryckaert-Bell. atoms    8   11   14   16 global
>              1248  1251     1254  1256
>                      Ryckaert-Bell. atoms    8   11   14   17 global
>              1248  1251     1254  1257
>                               LJ-14 atoms    8   15           global
>              1248  1255
>                               LJ-14 atoms    8   16           global
>              1248  1256
>                      Ryckaert-Bell. atoms    9    8   11   14 global
>              1249  1248     1251  1254
>                               LJ-14 atoms    9   14           global
>              1249  1254
> 
>                -------------------------------------------------------
>                Program mdrun_mpi, VERSION 4.5.4
>                Source code file: domdec_top.c, line: 356
> 
>                Fatal error:
>                49 of the 18125 bonded interactions could not be calculated
>                because some atoms involved moved further apart than the
>                multi-body cut-off distance (1.25 nm) or the two-body cut-off
>                distance (1.25 nm), see option -rdd, for pairs and
>             tabulated bonds
>                also see option -ddcheck
>                For more information and tips for troubleshooting, please
>             check
>                the GROMACS
>                website at http://www.gromacs.org/Documentation/Errors
> 
> 
>            OK, your system blew up.
> 
> 
> 
>                mdp file:
> 
>                ;        Bonds
>                constraints             = none                  
>              constraint-algorithm = lincs        
>                ;        Run control                       integrator    
>                  =  md                       dt                  =
>              0.001                  nsteps              =  500000 ;5000
>                                      nstcomm             =  100        
>                  
>                ;        Output control
>                nstenergy           =  100                  ; frequency
>             to write
>                energies to energy file. i.e., energies and other
>             statistical data
>                are stored every 10 steps
>                nstxout             =  100;1                nstvout      
>                   =  0
>                nstfout             =  0
>                nstlog              =  1000                 ; frequency
>             to write
>                energies to log file
>                nstxtcout          =  1000              
>                ;        Neighbor searching
>                nstlist             =  10                   ns_type      
>                   =  grid              
>                ;        Electrostatics/VdW
>                coulombtype         =  Shift                    
>              vdw-type            =  Shift                rcoulomb-switch
>                 =  0                      rvdw-switch         =  0.9 ;0
>                                        
>                ;        Cut-offs
>                rlist               =  1.25                  rcoulomb    
>                    =  1.0            rvdw                =  1.0        
>                  
>                ;        Temperature coupling       Tcoupl              =
>              v-rescale               tc-grps             =  System
>                tau_t               =  0.1      ref_t               =  300  
>                ;        Pressure coupling
>                Pcoupl              =  Parrinello-Rahman            
>             Pcoupltype          =  isotropic                  tau_p    
>                       =  1                          compressibility    
>             =  4.5e-5 4.5e-5           ref_p               =  10        
>                    
>                ;        Velocity generation                 gen_vel    
>                     =  yes                    gen_temp            =
>              300.0                   gen_seed            =  173529      
>                    
> 
> 
>            Generating velocities and compressing from an unequilibrated
>         initial
>            conformation in the same run is asking for trouble, and sometimes
>            you're observing it. See
>          
>          http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation.
>            Equilibrate first. Then slowly change the conditions so that
>         you're
>            never all that far from equilibrium, and reach your destination.
> 
>            Hello Mark,
> 
>            My box of alkane was already equilibrated using a NVT run. I just
>            have to increase the density.
>            After NVT run, do I have to turn off gen_vel             =
>          yes      for NPT run? Is this necessary for all NPT runs?
> 
> 
>     You don't re-generate velocities between simulation intervals, or
>     else you destroy any semblance of an equilibrated state you achieved
>     before.  Proper preservation of the previous ensemble is achieved
>     through grompp -t with a checkpoint file.
> 
>     Sorry but to double check this, for NPT I need command below?
> 
> 
> grompp -f md.mdp -c last-frame-from-NVT.gro -p .top  -t trajectory-file- 
> from- NVT.trr   -o md-NPT.tpr
>  
> How  do I introduce checkpoint file from previous NVT run?
> 

Like I said, pass the checkpoint file (.cpt) to the -t flag to preserve state 
information.

> BTW, by PR I meant parrinello rahman. sorry for confusion.

OK, that makes more sense.  Please avoid unnecessary abbreviations :)

-Justin

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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



More information about the gromacs.org_gmx-users mailing list