Re: Polymer Layer/ Cutoff

From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Thu May 15 2014 - 18:00:42 CDT

Are you trying to simulate bulk liquid PFP? If yes, follow the procedure
in the CGenFF paper (using a cubic box). Also, you're precariously close
to the experimental boiling point, and the force field's boiling point
could easily be a few degrees lower.

If you're trying to accomplish something else, please consult with your
advisor. I suspect fundamental flaws in the physics of what you're trying
to do.

On 05/15/2014 05:13 PM, Rawan Al Nsour wrote:
> nothing above or below. just the polymer
>
>
> On Thu, May 15, 2014 at 3:34 PM, Kenno Vanommeslaeghe
> <kvanomme_at_rx.umaryland.edu <mailto:kvanomme_at_rx.umaryland.edu>> wrote:
>
> 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>
> <mailto: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>
> <mailto:alnsourra_at_vcu.edu <mailto:alnsourra_at_vcu.edu>>
>
> 401 W. Main Street, Room E3216
> P.O. Box 843015
> Richmond, Virginia 23284-3015
>
>
>
>
>
>
>
>
>
>
>
> --
> 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
>
>
>
>
>
>
>

This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:20:48 CST