[gmx-users] potential energy

[Meenakshi Rajput]

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??
>>
>