[gmx-users] gmx potential calculation with one sodium ion at the center of box

이연경 koki0724 at naver.com
Mon Mar 12 14:34:33 CET 2018

Dear Gromacs users, 

I’m testing a simple system that has one sodium ion to check electric field. (NVE simulation)
I used gmx potential- to check electric field.

According to gromacs manual 5.0.4 (p.8), ‘the potential of an electronic charge at distance of 1nm equals f ~140 units ~ 1.4V.’

I expected the result graphs would represent gaussian form with the highest value of 1.4V/nm, but it only calculated upper side of box from where the sodium ion was and the highest value was 0.8V/nm. ( linear graph with minus slope ) (x axis is BOX(nm) )

Why does gromacs potential not calculate down side of the sodium ion? And why was the value different from that of the manual?
I’m waiting for your answer.
Thanks for your time :)
Best regards,

 YK Lee

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