[gmx-users] Epsilon-rf

[Maryam Kowsar]

Dear Alex,
I have another question related to coulombtype selection. I dont want to
use pbc in my system so, PME and Ewald are not good choices. If I use
Reaction-field-zero and define a rcoulomb equal to my system size ( since
epsilon-rf is 0 out of cutoff size) would it do the same work as finding
epsilon-rf in generalized field reaction?
THANKS!

On Tue, Apr 28, 2015 at 10:22 PM, Maryam Kowsar <maryam.kowsar at gmail.com>
wrote:

> If I use PME there's no need to find epsilon-rf, but I have to change some
> other parameters. I will try it.
> Thank you very much Alex!
>
> On Tue, Apr 28, 2015 at 11:31 AM, Alex <nedomacho at gmail.com> wrote:
>
>>  With reaction-field-zero, the only option is epsilon-rf=0. That aside,
>> if the nanotube is small, i would use cut-off electrostatics with
>> coulomb-cutoff comparable to the length of the tube.
>>
>> If the tube is long, I would use standard pme. I would be extremely
>> careful about using truncated electrostatics in general. Given the above, I
>> am not sure I understand what's there to calculate, unless you mean running
>> a simulation and _obtaining_ a dielectric property as a result. In that
>> case, given you system, it is a completely different discussion.
>>
>>
>> Alex
>>
>>
>> MK> Not a poorly formed but a general question!
>>
>> MK> You are right about reaction-field-zero. reaction-field leads to
>>
>> MK> bad energy conservations. So, I decided to use reaction-field-zero
>>
>> MK> but as I have some charges I don't know what to do with them. I
>>
>> MK> have a CNT in which there are some ions. I want to calculate the
>>
>> MK> epsilon-rf for it. I don't know if epsilon-rf belongs to the whole
>>
>> MK> system and if so, how I should calculate it.
>>
>> MK> thanks!
>>
>>
>>
>>
>> MK> On Tue, Apr 28, 2015 at 10:50 AM, Alex <nedomacho at gmail.com> wrote:
>>
>> MK> That's a pretty poorly formed question, including the part where you
>>
>> MK> actually "calculate" the epsilon-rf value. Can you please try again
>> with
>>
>> MK> a description of your system?
>>
>>
>> MK> Alex
>>
>>
>> MK>> Dear all,
>>
>> MK>> I use reaction-field-zero as the coulombtype for my system. I wonder
>> how I
>>
>> MK>> should choose the right epsilon-rf. How can I calculate the
>> dielectric
>>
>> MK>> constant in the system?
>>
>> MK>> Thank you.
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>>
>> Best regards,
>>
>>  Alex                            mailto:nedomacho at gmail.com
>> <nedomacho at gmail.com>
>>
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>