[gmx-users] Positive energy .

[Rasoul Nasiri]

Why do you think positive values are doubtful?
What matters are energy differences between different snapshots
The absolute energy is meaningless in the FF framework.

Rasoul


On Tue, May 13, 2014 at 3:59 PM, Bryan Roessler <roessler at uab.edu> wrote:

> 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
> > --
> > 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-request at gromacs.org.
> >
> --
> 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-request at gromacs.org.
>