MD melting problem

4985... at qq.com 4985... at qq.com
Thu May 3 12:18:49 UTC 2018


Hello, Matt, thanks for the answer, but I am a little confused. Should I 
use the STRESS_TENSOR DIAGONAL_ANALYTICAL instead of the MM force field or 
to analysis the stress changing during the simulation?

在 2018年5月3日星期四 UTC+8下午6:04:44,Matt W写道:
>
> Probably unrelated to you actual question, but changing to
>
> STRESS_TENSOR DIAGONAL_ANALYTICAL
>
> should give you a big speed up.
>
> Matt
>
> On Thursday, May 3, 2018 at 1:37:55 AM UTC+1, 498... at qq.com wrote:
>>
>> Hello, everyone, I want to simulate the melting structure of molten 
>> salts. The simulation began with  crystal structure and temperature was set 
>> at 3000 K in NPT ensemble, which is far more higher than the melting point. 
>> However, the result is frustrating. After 100 ps runs, the ions still in 
>> crystal structure. The parameters in the force field is in published paper 
>> and widely used, so I wonder somewhere in the input file is wrong. The file 
>> is listed below, could anyone tell me the possible problems? Thanks very 
>> much.
>>
>>
>> &GLOBAL                         ! Section with general information 
>> regarding which kind of simulation to perform an parameters for the whole 
>> PROGRAM
>>   PROJECT C6                    ! Name of the project. This word will 
>> appear as part of a name of all ouput files (except main ouput file, 
>> specified with -o option)
>>   RUN_TYPE MD           ! Molecular Dynamics
>>   PRINT_LEVEL low
>> &END GLOBAL
>>
>>
>> &FORCE_EVAL ! This section defines method for calculating energy and 
>> forces
>>   METHOD FIST ! Using Molecular Mechanics
>>   STRESS_TENSOR NUMERICAL
>>   &MM
>>     &FORCEFIELD ! This section specifies forcefield parameters
>>       ..........
>>     &END FORCEFIELD
>>     &POISSON ! This section specifies parameters for the Poisson solver
>>       &EWALD ! This section specifies parameters for the EWALD summation 
>> method (for the electrostatics)
>>         EWALD_TYPE none ! Standard real-space coulomb potential is 
>> computed together with the non-bonded contributions.
>>       &END EWALD
>>     &END POISSON
>> &NEIGHBOR_LISTS
>>   GEO_CHECK TRUE
>>   NEIGHBOR_LISTS_FROM_SCRATCH TRUE
>>   VERLET_SKIN 1
>>     &END NEIGHBOR_LISTS 
>>   &END MM
>>   &SUBSYS ! This section defines the system
>>     &CELL ! Unit cell set up
>>       ABC 22.56 22.56 22.56 ! Lengths of the cell vectors A, B, and C
>>       ALPHA_BETA_GAMMA 90.0 90.0 90.0
>>       PERIODIC  XYZ
>>     &END CELL
>>     &TOPOLOGY 
>>      COORD_FILE_NAME  NaCl.xyz 
>>      COORDINATE xyz ! The type of the file  is XYZ
>>     &END TOPOLOGY
>>   &END SUBSYS
>> &END FORCE_EVAL
>>
>> &MOTION ! This section defines a set of tool connected with the motion 
>> of the nuclei.
>>  &PRINT
>>  &TRAJECTORY
>>     LOG_PRINT_KEY T
>>     FORMAT XMOL
>>     &EACH
>>      MD 10000
>>     &END EACH
>>     ADD_LAST NUMERIC   
>>  &END TRAJECTORY
>>  &END PRINT
>>  &MD 
>>     ENSEMBLE NPT_I
>>     TEMPERATURE 3000
>> &BAROSTAT
>>   PRESSURE 0
>>   TEMPERATURE 3000
>> &END BAROSTAT
>> &THERMOSTAT
>>         TYPE NOSE
>>          REGION GLOBAL
>>          &NOSE
>>            TIMECON 100
>>            LENGTH 3
>>            MTS 2
>>          &END NOSE
>>      &END THERMOSTAT
>> TIMESTEP 1.0
>> STEPS 100000
>>  &END MD
>>
>>   &PRINT
>>     &RESTART
>>       LOG_PRINT_KEY T
>>       &EACH
>>         MD 10000
>>       &END EACH
>>       ADD_LAST NUMERIC
>>     &END RESTART
>>   &END PRINT
>> &END MOTION
>>  &END
>> &END MOTION
>>
>>
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