[gmx-users] Is there any difference with gromacs and other MD programs?

설진규 (자연과학부) seoljk0609 at unist.ac.kr
Mon Jan 22 06:44:05 CET 2018

Dear gmx users,

I’ve started to run MD simulation of ion aggregation of aqueous solution. (JCP 145, 174501 (2016))

So I followed adding initial molecules(I gained BF4 ion topology from https://atb.uq.edu.au/molecule.py?molid=26889) , em, ensembles and md simulation. Then I calculated RDF but their g(r) values of O...O(figure 1-a in given journal) are slightly different between simulation on paper and I did.

My simulation reports g(0.464)=1.044.

I might guess the problem is that I used gromacs with gromos54a7 force field and the paper simulated with AMBER. I thought the molecules of the system is so simple that those force fields couldn’t be too different.

My questions are;

1. Are there any difference of calculating method between GROMACS and AMBERMD? If so, how can I find its details?

2. If I select AMBER force field and edit topology and run it by GROMACS, can I solve the simulation with completely same result with this journal?

Thank you.


Jingyu Seol.

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