Re: Polymer Layer/ Cutoff

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Thu May 15 2014 - 14:34:00 CDT

What's above and below the layer?

Also, please reply to the list rather than personal e-mail (hint to the
list admin: Majordomo has an option to override the Reply-To: address!)

On 05/15/2014 01:19 PM, Rawan Al Nsour wrote:
> Thank you Dr. Kenno.
>
> I will increase the y dimension.
> In fact, I am working on a teflon layer. this layer made of 196 chain of
> c5f12, I built the box based on the experimental density
>
> ‚Äč
>
>
>
>
> On Thu, May 15, 2014 at 12:58 PM, Kenno Vanommeslaeghe
> <kvanomme_at_rx.umaryland.edu <mailto:kvanomme_at_rx.umaryland.edu>> wrote:
>
> The nonbonded cutoff is an integral part of the force field and
> changing it will affect properties. The right solution is to increase
> the dimensions of your simulation system to be larger than the cutoff
> by a big enough MARGIN (hint, hint; please consult the relevant
> documentation). And yes, this means there's a minimum linear dimension
> of bulk phase systems that can be simulated using a given FF. And even
> it that wouldn't be the case, 7.3A too small anyway; you'll get PBC
> artifacts.
>
> Out of curiosity, why are you trying to simulate a square pancake?
>
>
>
>
> --
> Rawan Al Nsour
> Ph.D. Candidate
> Department of Mechanical and Nuclear Engineering
> School of Engineering, Virginia Commonwealth University
> E-mail: alnsourra_at_vcu.edu <mailto:alnsourra_at_vcu.edu>
> 401 W. Main Street, Room E3216
> P.O. Box 843015
> Richmond, Virginia 23284-3015
>
>
>
>
>
>
>

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