[gmx-users] potential energy

[Justin Lemkul]

On 8/11/14, 1:06 PM, Meenakshi Rajput 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.
>

The proper settings (in Gromacs 5.0) for CHARMM36 are:

cutoff-scheme = Verlet
vdwtype = cutoff
vdw-modifier = force-switch
rlist = 1.2
rvdw = 1.2
rvdw-switch = 1.0
coulombtype = PME
rcoulomb = 1.2
DispCorr = no

We have verified that the above reproduce the forces using CHARMM 
vfswitch/pmewald settings that are used to derive the force field.

-Justin

>
> 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

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