Re: Polymer Layer/ Cutoff

From: Rawan Al Nsour (alnsourra_at_vcu.edu)
Date: Thu May 15 2014 - 16:13:58 CDT

nothing above or below. just the polymer

On Thu, May 15, 2014 at 3:34 PM, Kenno Vanommeslaeghe <
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>> 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
>>
>>
>>
>>
>>
>>
>>
>>
>

-- 
Rawan Al Nsour
Ph.D. Candidate
Department of Mechanical and Nuclear Engineering
School of Engineering, Virginia Commonwealth University
E-mail: alnsourra_at_vcu.edu
401 W. Main Street, Room E3216
P.O. Box 843015
Richmond, Virginia 23284-3015

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