Re: [gmx-users] npt simulation error

2017-08-16 Thread 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  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  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
>>>
>>> 303 Engel Hall
>>> 340 West Campus Dr.
>>> Blacksburg, VA 24061
>>>
>>> jalem...@vt.edu | (540) 231-3129
>>> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>>>
>>> ==
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>>>
>>
>>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
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>



-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu *
* Skype: parash.khan2*
*Cell: +12085967165*
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Re: [gmx-users] npt simulation error

2017-08-16 Thread Justin Lemkul 



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  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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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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

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==

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Re: [gmx-users] npt simulation error

2017-08-15 Thread Mohammad Zahidul Hossain Khan 
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r= 4


On Tue, Aug 15, 2017 at 6:18 PM, Justin Lemkul  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
>
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalem...@vt.edu | (540) 231-3129
> http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
>
> ==
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>



-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu *
* Skype: parash.khan2*
*Cell: +12085967165*
-- 
Gromacs Users mailing list

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Re: [gmx-users] npt simulation error

2017-08-15 Thread Justin Lemkul 



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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==
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[gmx-users] npt simulation error

2017-08-15 Thread Mohammad Zahidul Hossain Khan 
Dear Sir

I am trying to simulate protein_ligand complex using epsilon = 4 and it is
giving the below error

*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
-- 


*Mohammad Zahidul Hossain Khan Graduate student**Department of Physics*
*Email: khan5...@vandals.uidaho.edu *
* Skype: parash.khan2*
*Cell: +12085967165*
-- 
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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