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 -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Virginia Tech Department of Biochemistry 303 Engel Hall 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.biochem.vt.edu/people/faculty/JustinLemkul.html ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
