[gmx-users] Positive PE in minimization step of ionic liquid BMIM PF6

[David van der Spoel]

On 22/04/17 14:48, Abhishek Banerjee wrote:
> Hi
>     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
> interactions
> 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.
http://www.icm.uu.se