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Re: [lammps-users] Ensemble choices for MSD calculation

# Re: [lammps-users] Ensemble choices for MSD calculation

 From: Axel Kohlmeyer Date: Wed, 22 Nov 2017 07:25:44 -0500

On Wed, Nov 22, 2017 at 6:15 AM, Hai Hoang wrote:
Hi,

Temperature you studied is rather high, please check effect of time step.

1. Use fix temp/rescale with fix NVE to control the temperature precisely.  But I learned from mail-list that this is not usually recommended.
-->> Yes, should not use this fix when study the transport properties (You can find some discussions in some text books, such thermostat does not discribe the system in true NVT ensmble). Try to test "fix langevin"
2. Use fix NVT to calculate MSD rather than fix NVE. It may require a bigger Tdamp to decrease temperature fluctuation.
-->> Should use NVT, but check effect of time step and Tdamp.
In fact, you can also use NPT... Results are similar.

for correct MSD calculations, a weakly coupled thermostat is needed, and then ​the fluctuations ​with either fix nvt or fix nve should be of comparable magnitude. if they are not, then you don't have a weakly coupled thermostat and thus the thermostat settings should be adjusted accordingly or there are some general problems with the equilibration workflow, that need to be addressed. there is not enough information to tell which is happening. the "natural" magnitude of temperature fluctuation depends on (as mentioned) the temperature, the strength of the interactions and the size of the system.

axel.

Best,

On Wed, Nov 22, 2017 at 8:45 AM, 284237308@...1204... wrote:
Dear my friends,
I want to calculate the diffusion coefficient of hydrogen in water at infinite dilution. My method is based on the example in LAMMPS files. First,  I use fix NVE and fix langevin to equilibrate  the whole system. Then I use fix NVT to control the temperature. And I use fix NVE to compute MSD.
But from the results, in NVE ensemble, the temperature fluctuate a little wildly. For example, when I set 1000K, the temperature may go down most to 940K. And my work is focusing on a series of temperature setting with 700,750,800,850....,1150 and 1200K. What is confusing is that the diffusion coefficient at 1050K is lower than 1000K at same system density. I think this is because the temperature fluctuation in NVE ensemble. Thus I cannot accept this temperature fluctuation. Now I think of two solutions.
1. Use fix temp/rescale with fix NVE to control the temperature precisely.  But I learned from mail-list that this is not usually recommended.
2. Use fix NVT to calculate MSD rather than fix NVE. It may require a bigger Tdamp to decrease temperature fluctuation.
Can you give me some advice about these two solutions? Or any other suggestion?
Thanks a lot.

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