H Justin, 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 <jalem...@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 outdated (which is likely the case with most/all of the AMBER force 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 > > -- > ================================================== > > 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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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. > -- Netaly -- 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.