MD melting problem

[jie wu]

Thanks for the explanation, it is really helpful, I will convert.

在 2018年5月3日星期四 UTC+8下午8:43:17，Matt W写道：
>
> Your input file has
>
> STRESS_TENSOR NUMERICAL
>
> this is probably very expensive. You don't need the full stress tensor for 
> NPT_I, and analytical should be faster and more accurate than numerical (if 
> available for your forcefield)
>
>
> On Thursday, May 3, 2018 at 1:18:49 PM UTC+1, jie wu wrote:
>>
>> 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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