[gmx-users] Energy minimization

[Justin Lemkul]

On 7/8/15 8:03 PM, Malihe Hasanzadeh wrote:
> Hi,
> I want to do MD simulation of protein-DNA-ligand using Gromacs 5.0.4.,when I
> do energy minimization, my system is converged but has positive potential
> energy. also this step only takes 3 second! for next step (pr), gives error:
> your system is not equilibrated well and blowing up! I chcked my em.pdb
> file and
> I saw the Sol box is separated from protein and DNA!

This is probably just a PBC effect; use trjconv.

> Could you please help me, what should I do?what part of my set is wrong?
>

Your EM outcome suggests an unresolvable clash in the system, so it's pointless 
to try dynamics unless you get a force below the specified tolerance (or at 
least of some other reasonable magnitude).  mdrun tells you where the maximum 
force is, so that's where you should start looking.  Beyond that, you'll have to 
give us a complete description of what you've done to prepare the system, 
parametrize the ligand, etc.  General troubleshooting that you should always follow:

http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System

> my em.mdp:
> define = -DFLEXIBLE

I'm assuming you're trying to use rigid water during the subsequent dynamics 
(you should), so you'll want to re-minimize without flexible water. 
Occasionally, the waters distort and SETTLE cannot fix the geometry.  This is 
not likely the source of your problem, just an FYI.

-Justin

> integrator = cg ; steep
> nsteps = 4000
> nstlist = 1
> constraints = none
> emtol = 100.0
> nstcgsteep = 10 ; do a steep every 10 steps of cg
> emstep = 0.01 ; used with steep
> nstcomm = 1
> nstcalcenergy = 1.2
> ewald_rtol = 1e-05
> coulombtype = PME
> cutoff-scheme = Group
> ns_type = grid
> rlist = 1.4
> rcoulomb =1.4
> rvdw = 1.4
> Tcoupl = no
> Pcoupl = no
> gen_vel = no
> nstxout = 0 ; write coords every # step
> optimize_fft = yes
>
> Sincerely,
> Malihe
>

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

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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