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

Justin Lemkul jalemkul at vt.edu
Mon Jan 22 13:51:53 CET 2018

On 1/22/18 12:43 AM, 설진규 (자연과학부) wrote:
> 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.

That's a bad assumption. Each force field is parametrized under 
different conventions and different target data, so you should not 
expect equivalent results.

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

Refer to each program's reference manual and published literature. Every 
MD engine is a little different in its algorithms, features, 
optimizations, etc.

> 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?

Within statistical error, yes.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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