[gmx-users] Why did the aggregate of salt happen when I used Gromacs to perform the simulation in 1.5 M KCl solution?
David van der Spoel
spoel at xray.bmc.uu.se
Sun Nov 29 23:04:58 CET 2015
On 29/11/15 19:01, Smith, Micholas D. wrote:
> Dear Shaoqu Xie,
> You should check your force-field parameters and water model, typically the limit for simulating aqueous salt solutions is ~0.5M. Take a quick search on the ACS publication webpage for more details (I currently don't have access at the moment to give you the exact citation).
This is a known bug with certain Amber force fields. Don't know about
oplsaa but it might even use the same salt parameters. Try google.
> Micholas Dean Smith, PhD.
> Post-doctoral Research Associate
> University of Tennessee/Oak Ridge National Laboratory
> Center for Molecular Biophysics
> From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of xieshaoqu at qq.com <xieshaoqu at qq.com>
> Sent: Friday, November 27, 2015 2:35 AM
> To: gromacs.org_gmx-users
> Subject: [gmx-users] Why did the aggregate of salt happen when I used Gromacs to perform the simulation in 1.5 M KCl solution?
> Dear expert,
> My molecular dynamics simulation was performed in 1.5 M KCl aqueous solution or 1.5 M KCl ethanol solution (v:v=1:1). The oplsaa force field and spc216.gro were used (300k,1bar). The results showed that KCl aggregated with 10 ns of simulation. Could you tell me why the aggregate of salt happened when I used Gromacs to perform the simulation in 1.5 M KCl solution. Is it meaningful to use Gromacs to simulate phase splitting induced by salting-out method? The aggregate was much more serious. Is Gromacs workable to simulate the salting-out of ethanol?
> Kind regards,
> Shaoqu Xie, PhD
> School of Chemistry & Chemical Engineering, South China University of Technology, No. 381 Wushan Road, Guangzhou 510640, P. R. China
> Phone: 15017504150
> Email: xieshaoqu at foxmail.com;15017504150 at 163.com
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David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
spoel at xray.bmc.uu.se http://folding.bmc.uu.se
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