[gmx-users] Dielectric constant calculation

[David van der Spoel]

On 15/10/16 10:02, Thejus Kartha wrote:
> Greetings!
> I was trying to calculate the dielectric constant of my system (1,4-dioxane and water), and I have encountered some problems. I gave the command to calculate dipole moment and related data, since it is a prerequisite for the dielectric calculation:
>
> gmx dipoles -f sol1ns2.trr -s sol1ns2.tpr -o dipac.xvg -eps diel_1.xvg -a muavers.xvg -d dipdist.xvg -P 1 -corr total -c dipcorr.xvg
> which ran perfectly, providing me with 5 .xvg files, as it should. Now, following this, I typed in:
> gmx dielectric -f dipcorr.xvg -d deriv.xvg -o epsw.xvg -c cole.xvg
> which gave me the error and the warning:---------------------------------------------------------------------------------------------------
> WARNING: non-polarizable models can never yield an infinite
> dielectric constant that is different from 1. This is incorrect
> in the reference given above (Spoel98a).---------------------------------------------------------------------------------------------------
> *** Error in `gmx': malloc(): smallbin double linked list corrupted: 0x00000000011191f0 ***
> Aborted (core dumped)
> ---------------------------------------------------------------------------------------------------Can you please let me know where I am going wrong? I understand that there's something called the reaction field epsilon value, which is where I could have gone wrong, as I did not specify it in the first command.
>
> Thanks in advance,Thejus Kartha.
>
This has been fixed in the latest gromacs 5.1.4 and 2016. If you just 
want the dielectric constant at zero frequency you don't need to run gmx 
dielectric at all however.

-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se