[gmx-users] clustering of ions during NPT simulation

Justin Lemkul jalemkul at vt.edu
Fri Jun 28 19:15:26 CEST 2019

On 6/27/19 8:44 AM, Netaly Khazanov wrote:
> Hi All,
> I perform simulation of a transmembrane protein in a membrane in 1M
> concentration of NaCl.
> During the simulation, I noticed that ions began to cluster and they are
> not evenly spread after 10 ns. Is it a problem or I can proceed further?

Some ion parameters are known to aggregate but this issue is long since 
solved. You don't state which parameters you used, but if they are 
outdated (which is likely the case with most/all of the AMBER force 
fields provided with GROMACS), you need to use better parameters.



Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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


More information about the gromacs.org_gmx-users mailing list