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mks #17330 06/18/08 05:10 PM
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The error in the integration and thus the accuracy of the simulation is a function of the timestep; a larger timestep has a larger error.

rmv #17331 06/18/08 06:05 PM
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Thanks for your reply. One more thing, does this error related to NPT vs NVT ? I am using NPT with 2fs for MM-PBSA calculation and want to be little sure about it.

mks #17332 06/18/08 06:15 PM
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I thought MM-PBSA was an implicit solvent model; I'm not sure I follow why it would be used for NPT. I would in general recommend 1 fs for condensed phase systems (explicit solvent), esp. when performing NPT or NVT dynamics via the extended system CPT code (pressure.doc).

rmv #17333 06/18/08 07:12 PM
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Quote:

In general, a smaller timestep gives a more accurate integration, and 0.5 fs has been used at times. The dilemma is that it doubles the CPU time for each ps of simulation time, so 1.0 fs and even 2.0 fs are more prevalent.




Accurate compared to what?

The point of using 1.0 fs (instead of 2.0 fs or, for that matter, 0.5 fs) is simply to be consistent with the simulation protocol MacKerrel and collaborators have used to test the properties of their force fields.

Other than to simulate fast X-H vibrations (which would otherwise not be numerically stable), I don't see any good reason to use a 0.5 fs time step. The force field will not get better if you decrease the time step.


Guillaume Lamoureux
Department of Chemistry and Biochemistry
Concordia University, Montreal, Canada
http://faculty.concordia.ca/glamoure
rmv #17334 06/18/08 07:27 PM
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I am running simulation in explicit solvent to get correct sampling. For MM-PBSA, I will remove the water from explicit solvent trajectories.

Thanks for your reply.

lamourgu #17335 06/18/08 08:13 PM
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The point of using 1.0 fs (instead of 2.0 fs or, for that matter, 0.5 fs) is simply to be consistent with the simulation protocol MacKerrel and collaborators have used to test the properties of their force fields. Other than to simulate fast X-H vibrations (which would otherwise not be numerically stable), I don't see any good reason to use a 0.5 fs time step. The force field will not get better if you decrease the time step.

I was mainly speaking about the accuracy of the integration itself, which is known to be timestep dependent. Naturally, the timescale of the motions being sampled has a bearing on this.

The force field development strategy is certainly another good reason to use 1 fs, but that choice in turn was based on the accuracy of the integration. I agree that there's usually not much benefit to using 0.5 fs, and probably none at all if SHAKE was used to constrain X-H bonds.

(I also don't think that all of FF development was done at 1 fs, although most of the more recent additions have been.)

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