[gmx-users] Positive PE in minimization step of ionic liquid BMIM PF6
David van der Spoel
spoel at xray.bmc.uu.se
Sat Apr 22 17:28:07 CEST 2017
On 22/04/17 14:48, Abhishek Banerjee wrote:
> I am new to Gromacs. I am trying to simulate ionic liquids BMIM PF6.
> First I made a simulation box with 128 ion pairs with packmol. *Then I did
> energy minimization. But I got positive PE*. I also did equilibration with
> npt and got reasonable density. *Is it normal for ionic liquids?* I
> searched a lot but did not get any answer.
Usually not a problem, since it depends on the intramolecular energy. I
suspect you have a large positive 1-4 Coulomb energy in BMIM.
> Steepest Descents converged to Fmax < 1000 in 269 steps
> Potential Energy = 1.0977283e+05
> Maximum force = 7.7167487e+02 on atom 3418
> Norm of force = 7.8315048e+01
> Here is my .mdp file
> integrator = steep
> emtol = 1000.0
> emstep = 0.02
> nsteps = 50000
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist = 10
> cutoff-scheme = Verlet
> ns_type = grid ; Method to determine neighbor list
> (simple, grid)
> coulombtype = PME ; Treatment of long range electrostatic
> rcoulomb = 1.4 ; Short-range electrostatic cut-off
> rvdw = 1.4 ; Short-range Van der Waals cut-off
> pbc = xyz ; Periodic Boundary Conditions (yes/no)
> Hope some one will help me to sort out the problem. Thanks for your time.
> Dr. Abhishek Banerjee
> Young Scientist, MRI-MRS centre
> Dept. of Chemistry, IIT Madras
> Chennai - 600036, Tamil Nadu, India
> Mob. No. 07598373142
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
More information about the gromacs.org_gmx-users