[gmx-users] npt simulation error

[Mohammad Zahidul Hossain Khan]

Dear Sir

Thank you very much for your response. Actually, I need dielectric constant
= 4 for coulomb force. I have no idea where should I give 4. I thought
*epsilon-r:
() *will work for me . So If I use epsilon-rf: 4, it will work. am I
correct?

On Wed, Aug 16, 2017 at 8:52 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/15/17 9:22 PM, Mohammad Zahidul Hossain Khan wrote:
>
>> ; Dielectric constant (DC) for cut-off or DC of reaction field =
>> epsilon-r                = 4
>>
>
> epsilon-r is used to change the relative dielectric constant; you
> shouldn't do this because it will fundamentally break the electrostatic
> convention used by all of the "usual" GROMACS force fields.
>
> If you're trying to alter reaction field properties, the keyword is
> epsilon-rf.  See the manual.
>
> -Justin
>
>
>> On Tue, Aug 15, 2017 at 6:18 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>> On 8/15/17 9:14 PM, Mohammad Zahidul Hossain Khan wrote:
>>>
>>> Dear Sir
>>>>
>>>> I am trying to simulate protein_ligand complex using epsilon = 4 and it
>>>> is
>>>> giving the below error
>>>>
>>>>
>>>> What is epsilon = 4?
>>>
>>> *2 particles communicated to PME rank 4 are more than 2/3 times the
>>> cut-off
>>>
>>>> out of the domain decomposition cell of their charge group in dimension
>>>> x*
>>>>
>>>> I have no idea how to solve this problem
>>>>
>>>>
>>>> Have you Googled it, or gone to the GROMACS error page, where lots of
>>> advice lives? ;)
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Assistant Professor
>>> Virginia Tech Department of Biochemistry
>>>
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>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
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>
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-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5121 at vandals.uidaho.edu <khan5121 at vandals.uidaho.edu>*
* Skype: parash.khan2*
*Cell: +12085967165*