[gmx-users] clustering of ions during NPT simulation
netalyk at gmail.com
Sun Jun 30 07:01:33 CEST 2019
I used amber99sb-ildn FF for the simulation.
Which parameters do you suggest to use?
Thanks in advance
On Fri, Jun 28, 2019 at 8:15 PM Justin Lemkul <jalemkul at vt.edu> wrote:
> 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 outdated (which is likely the case with most/all of the AMBER force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.
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> jalemkul at vt.edu | (540) 231-3129
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