[gmx-users] potential energy

[Meenakshi Rajput]

Thanks a lot Justin.
On Aug 11, 2014 10:36 PM, "Meenakshi Rajput" <ashi.rajput39 at gmail.com>
wrote:

> thanks...can you help me out with the mdp file settings with charmm force
> field(proteins)? I am a new user to gromacs and stuck here.
>
>
> On Mon, Aug 11, 2014 at 5:07 AM, Meenakshi Rajput <ashi.rajput39 at gmail.com
> > wrote:
>
>> 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??
>>>
>>
>