[gmx-users] grompp for minimization: note & warning

[Justin Lemkul]

On 9/16/13 3:06 AM, shahab shariati wrote:
> Dear Justin
>
> Very thanks for your reply.
>
> You said "I suspect your Gromacs version is somewhat outdated, as recent
> versions account for periodicity when
> making this check". I used 4.5.5 version of gromacs. What version of
> gromacs is more appropriate for my case.
>

When in doubt, always upgrade to the newest version, which is currently 4.6.3. 
I can't remember when the issue was fixed.

> Based on your suggestion, I used -maxwarn option for grompp. Then I used
> -nt 1 option for mdrun,
> but this step takes too long and
>
>
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+03
>     Number of steps    =        50000
> Warning: 1-4 interaction between 434 and 407 at distance 3.023 which is
> larger than the 1-4 table size 2.200 nm
> These are ignored for the rest of the simulation
> ********************   This usually means your system is exploding,
> ********************
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
>
> step 23: Water molecule starting at atom 10613 can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
>
> 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.
>
> Steepest Descents converged to machine precision in 2122 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  =  1.4310875e+05
> Maximum force     =  2.7179752e+04 on atom 5271
> Norm of force     =  4.0253470e+02

In this case, it is pretty clear that there is actually something wrong with the 
input coordinates.

> --------------------------------------------------------------------------------------
> my em.mdp file is as follows:
>
> 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
> nstlist        = 1            ; 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        ; Short-range electrostatic cut-off
> rvdw        = 1.2        ; Short-range Van der Waals cut-off
> pbc            = xyz         ; Periodic Boundary Conditions
> --------------------------------------------------------------------------------------
> gro, edr, trr and lof file were created.
>
> I increased emstep from 0.01 to 0.1 and I used constraints = none in mdp
> file, but result are the same.
>

Increasing emstep does not make sense.  If anything, you should be decreasing it 
to try to take smaller steps and resolve clashes.  In any case, the output tells 
you where the maximum force is.  Fire up your favorite visualization software, 
look at that atom and the things around it, and figure out what is going on.

> Is this minimization completely true?
> Can I use created gro file of this minimization for next step
> (equilibration)?
>

No, the forces are far too high to be useful.  Anything you do will simply crash.

-Justin

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

Justin A. Lemkul, Ph.D.
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

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