MD melting problem
jie wu
4985... at qq.com
Thu May 3 12:56:44 UTC 2018
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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