[gmx-users] NPT for compressing

Elisabeth katesedate at gmail.com
Sun May 22 04:24:53 CEST 2011


On 21 May 2011 19:02, Justin A. Lemkul <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>> 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?

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

>
>>
>>
>>>    When I use constraints for all-bonds and dt of 0.002 compressing
>>>    the box works well and I get density of above 600 SI which is the
>>>    actual density of alkane. Can any one help why setting no
>>>    constraints and dt=0.001 leads to the error message shown above.
>>>
>>
>>    You probably got lucky the first time and not the second. Or, your
>>    atom-atom bond interactions are no good.
>>
>>
>>     When no constraints is used PR doesnt work for compressing
>>>
>>
>>    So you want to restrain the positions of heavy atoms, but compress a
>>    pure system? This is contradictory. How do you want to decrease the
>>    volume if the atoms aren't allowed to move much?
>>
>>    I meant
>>
>>
>>    ;        Bonds
>>    constraints             = none
>>
>> not restraining position of atoms.
>>
>>
> Constraints and restraints are different.
>
> http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
>
> You said you were using position restraints (presumably that's what "PR"
> means).  If this is not the case, please provide an accurate description of
> what you're doing.
>
> -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
>
> ========================================
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