[gmx-users] problem during energy minimization

[Justin Lemkul]

On 12/9/14 6:51 AM, soumadwip ghosh wrote:
> Hello,
>          I am simulating a double stranded DNA in presence of choline. I am
> using CHARMM force field and GROMACS 4.5.6 for my simulations. I made the
> choline molecule as suggested by justin using CGenFF and included in my
> system by using -ci -nmol option of genbox. I am facing some problems in
> the energy minimization step which is as follows-
>
>
> Back Off! I just backed up emz.log to ./#emz.log.1#
> Reading file emz.tpr, VERSION 4.5.6 (single precision)
> Starting 80 threads
> Making 3D domain decomposition 5 x 4 x 4
>
> Back Off! I just backed up emz.trr to ./#emz.trr.1#
>
> Back Off! I just backed up emz.edr to ./#emz.edr.1#
>
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+03
>     Number of steps    =        50000
>
> Stepsize too small, or no change in energy.
> Converged to machine precision,
> but not to the requested precision Fmax < 1000
>
> Double precision normally gives you higher accuracy.
> You might need to increase your constraint accuracy, or turn
> off constraints alltogether (set constraints = none in mdp file)
>
> writing lowest energy coordinates.
>
> Back Off! I just backed up emz.gro to ./#emz.gro.1#
>
> Steepest Descents converged to machine precision in 331 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  =  5.4556762e+08
> Maximum force     =  4.0237480e+04 on atom 919
> Norm of force     =  4.8998334e+02
>
> NOTE: 7 % of the run time was spent communicating energies,
>        you might want to use the -gcom option of mdrun
>
> My minimization.mdp file is as follows-
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator      = steep         ; Algorithm (steep = steepest descent
> minimization)
> emtol           = 1000.0        ; Stop minimization when the maximum force
> < 1000.0 kJ/mol/nm
> emstep          = 0.01          ; Energy step size
> nsteps          = 50000         ; Maximum number of (minimization) steps to
> perform
>
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist         = 1             ; Frequency to update the neighbor list and
> long range forces
> ns_type         = grid          ; Method to determine neighbor list
> (simple, grid)
> rlist           = 1.0           ; Cut-off for making neighbor list (short
> range forces)
> coulombtype     = PME           ; Treatment of long range electrostatic
> interactions
> rcoulomb        = 1.0           ; Short-range electrostatic cut-off
> rvdw            = 1.0           ; Short-range Van der Waals cut-off
> pbc             = xyz           ; Periodic Boundary Conditions (yes/no)
> ~
>
>
> I read about 'blowing up' of the system but I dont know how to use double
> precission GROMACS. I cant figure out what the problem is. Is there
> anything wrong with the .mdp file? Is there anything wrong with my initial
> and solvated configurations? If not what is the way to get rid of this
> error?
>

Yes, your nonbonded parameters are wrong, though it's probably not the cause of 
the issue.  See http://www.gromacs.org/Documentation/Terminology/Force_Fields/CHARMM

To solve the issue, you have to do things scientifically - split the system into 
simpler components to narrow down the cause.  What is the atom on which Fmax is 
acting?  What is around it?  Are the bonded and nonbonded parameters correctly 
assigned for that atom and anything to which it is connected?  Test the ligand 
topology - does it minimize alone in vacuo, and in water?  Does the DNA minimize 
on its own?

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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