[gmx-users] 回复: Re: Implicit Solvent and Box Size

[Justin Lemkul]

On 10/7/19 10:40 PM, 张 卓 wrote:
> Dear Justin,
>
> I have tried implicit solvent without pbc or barostat. The box was not compressed but the molecules flew out of the box. I believe that it was because of nopbc box. Would you please give more information on why implicit solvent is used without pbc?

Because there's no need for it. In explicit solvent simulations, we use 
PME for long-range electrostatics and that requires PBC. In implicit 
solvent, there's no need (this is also a reason why implicit simulations 
have intrinsic accuracy issues).

Beyond that, regarding your observations, there is no box. The molecule 
is simply diffusing through space, which will happen in any simulation. 
In a simulation with PBC, this has the effect of the molecule crossing 
back and forth over borders ("jumping"), which simply doesn't happen in 
your case.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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