[gmx-users] MDP for DNA with ions

[Justin Lemkul]

On 6/22/17 9:21 AM, Sergio Manzetti wrote:
> Justin, I fixed the sim.mdp, however I realized I sent you the wrong mdp file, the one that gave DNA minimization problem is the EM.mdp
> 
> Which is this:
> 
> define =
> integrator = steep
> emtol = 100.0
> emstep = 0.001
> nsteps = 100000
> ; output frequency
> nstxout = 50
> nstvout = 0
> nstfout = 0
> nstlog = 50
> nstenergy = 50
> nstxtcout = 0
> xtc_grps = system
> ;
> nstlist = 10
> pbc = xyz
> rlist = 0.8
> cutoff-scheme = group
> coulombtype = PME
> rcoulomb = 0.8
> vdwtype = cut-off
> rvdw = 0.8
> DispCorr = EnerPres
> ;
> constraints = none
> constraint_algorithm = LINCS
> implicit_solvent = no
> E_x =
> E_y =
> E_z =
> 
> 
> However, it looks completely normal...
> 
> 
> Still the system is not apprently equilibrated
> 
> 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.
> This usually means that your system is not well equilibrated.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> 

Follow the link I provided before about diagnosing the problem.

-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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