[gmx-users] potential energy

[Justin Lemkul]

On 8/13/14, 1:28 AM, Meenakshi Rajput wrote:
> hi
> thanks for the charmm settings...but N atom and H atom of LYS 313 and ALA
> 364 are coming out of the complex. Can you tell me why is this happening?

No idea what that means.

> And in next positional restrained run and md simulation, charmm settings
> would be same or some difference should be there?
>

Always the same.  Nonbonded settings are a fixed feature of the force field, not 
the simulation process.

-Justin

>
> On Tue, Aug 12, 2014 at 10:33 PM, Meenakshi Rajput <ashi.rajput39 at gmail.com>
> wrote:
>
>> 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??
>>>>>
>>>>
>>>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================