[gmx-users] Dielectric constant calculation

Thejus Kartha thejuskartha at ymail.com
Sat Oct 15 10:04:38 CEST 2016


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.



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