[gmx-users] Dielectric constant

[Justin Lemkul]

On 10/21/16 2:45 AM, Thejus Kartha wrote:
> Well, Dr. Lemkul, I tried using:
> gmx trjconv -pbc whole
>
> on the .trr file of my previous output. But, running the dipoles command on this new whole molecules system doesn't give any different results. The value I get is exactly the same. So, what is to be done? Thanks in advance.

Have you checked the properties of a neat liquid of dioxane?  There's a lot of 
variables in a mixed solution.  You need to validate the topology using 
something very well defined, like the properties of the pure liquid.  If you can 
establish that everything there is sane, then you can move on to something more 
complex.

-Justin

> Thejus Kartha
>
>
>
>
>     On Friday, 21 October 2016 7:55 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> Please keep the discussion on the list.
>
> On 10/20/16 10:20 PM, Thejus Kartha wrote:
>> Yes, Dr. Lemkul. I have done a complete simulation set. I don't think there's
>> anything wrong with the molecules as such.
>>
>
> mdrun writes broken molecules (across PBC).  You need to make them whole again
> with trjconv before doing analysis that depends on the positions of the charges.
>
> -Justin
>
>>
>>
>> On Friday, 21 October 2016 7:48 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>
>>
>> On 10/20/16 8:51 PM, Thejus Kartha wrote:
>>> Hello there.
>>> While calculating the dielectric constant of a mixture of dioxane in water, I
>> am getting really absurd values- a 1% solution has about 101. The command I've
>> been using is the following:
>>>
>>> gmx dipoles -f sol1ns2.trr -s sol1ns2.tpr -o dipac.xvg -eps diel_1.xvg -a
>> muavers.xvg -d dipdist.xvg -P 1 -corr mol -c dipcorr.xvg
>>> Can you tell me where I'm going wrong? And also, if I add the additional
>> option of -epsilonRF 78 with it, the value shoots up to more than 200. How come?
>>
>>
>> Did you make your molecules whole prior to doing the analysis?
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu> |
>> (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>>
>> ==================================================
>>
>>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================