[gmx-users] Positive energy .

[Bryan Roessler]

Did you hit your nsteps limit? 20000 probably isn't enough steps to get
below 10 Fmax.

*Bryan Roessler | Graduate Research Assistant*
UAB | The University of Alabama at Birmingham
*uab.edu/cmdb <http://uab.edu/cmdb>*
Knowledge that will change your world


On Tue, May 13, 2014 at 8:30 AM, sujithkakkat . <sujithks58 at gmail.com>wrote:

> Dear all,
>
>     I am running simulations for a water-CO2 system using the OPLSAA
> forcefield, where I use TIP4P/Ice water model and the EPM2 model for CO2.
> After energy minimization I found the value of potential energy to be
> positive, and also the maximum force value was high (I requested Fmax <10
> ). The values are as follows;
>
> Potential Energy    =  1.7600962e+05
> Maximum force     =  6.5140656e+01 on atom 1176
> Norm of force        =  8.7009411e+00
>
> Earlier when I did a simulation for gaseous CO2 using the same model, the
> potential energies were always positive. But I doubt whether the energy can
> be positive here.
>
> I want to make sure that I am not using any wrong parameters, before I
> proceed. Please comment.
>
>
>
>
>   My MDP file is as given below;
>
> ; Run control
> integrator = steep
> nsteps     = 20000
>
> ; EM criteria and other stuff
> emtol     = 10
> emstep   = 0.01
> niter        = 20
> nbfgscorr = 10
>
> ; Output control
> nstlog       = 1
> nstenergy = 1
>
> ; Neighborsearching and short-range nonbonded interactions
> nstlist    = 1
> ns_type = grid
> pbc       = xyz
> rlist       = 1.0
>
> ; Electrostatics
>
> coulombtype = PME
> rcoulomb      = 1.0
>
> ; van der Waals
>
> vdw-type     = switch
> rvdw-switch =0.8
> rvdw           = 0.9
>
> ; Apply long range dispersion corrections for Energy and Pressure
>
> DispCorr = EnerPres
>
> ; Spacing for the PME/PPPM FFT grid
>
> fourierspacing = 0.12
>
> ; EWALD/PME/PPPM parameters
>
> pme_order         = 6
> ewald_rtol          = 1e-06
> epsilon_surface  = 0
> optimize_fft        = no
>
> ; Temperature and pressure coupling are off during EM
>
> tcoupl  = no
> pcoupl = no
>
> ; Generate velocities to start
>
> gen_vel = no
>
> ; options for bonds
>
> constraints = all-bonds
>
> ; Type of constraint algorithm
>
> constraint-algorithm = lincs
>
> ; Do not constrain the starting configuration
>
> continuation = no
>
> ; Highest order in the expansion of the constraint coupling matrix
>
> lincs-order = 12
> --
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