[gmx-users] potential energy

[Meenakshi Rajput]

Thanks..but if potential becomes positive after energy minimisation run,
then is it normal or there is some prblm with my mdp file. I used the same
mdp file for this run also. I used charmm force field.
On Aug 11, 2014 2:32 PM, "Meenakshi Rajput" <ashi.rajput39 at gmail.com> wrote:

> hi users
> i have run energy minimisation of docked complex by using this min.mdp:-
>
> cpp        = /lib/cpp    ; Preprocessor
> include        = -I../top    ; Directories to include in the topology
> format
> integrator    = steep
> emtol        = 1000        ; Stop minimization when the energy changes by
> less than emtol kJ/mol.
> nsteps        = 200        ; Maximum number of (minimization) steps to
> perform
> nstenergy    = 10        ; Write energies to disk every nstenergy steps
> nstxtcout    = 10        ; Write coordinates to disk every nstxtcout steps
> xtc_grps    = Protein    ; Which coordinate group(s) to write to disk
> energygrps    = Protein    ; Which energy group(s) to write to disk
> nstlist        = 5        ; Frequency to update the neighbor list and long
> range forces
> ns_type        = grid      ; Method to determine neighbor list (simple,
> grid)
> rlist        = 1.2        ; Cut-off for making neighbor list (short range
> forces)
> coulombtype    = PME       ; Treatment of long range electrostatic
> interactions
> rcoulomb    = 1.2        ; long range electrostatic cut-off
> rvdw        = 1.2        ; long range Van der Waals cut-off
> constraints    = none        ; Bond types to replace by constraints
> pbc        = xyz        ; Periodic Boundary Conditions (yes/no0
> After the run, potential energy is negative. can you tell me whats the
> problem??
>