[gmx-users] System blowing up in Gromacsv5.0.5 but not in v4.5.4

[Justin Lemkul]

On 12/15/15 8:42 AM, NISHA Prakash wrote:
> Hi all,
>
> I am trying to simulate a protein using similar parameters as in the
> tutorial - Protein ligand by Justin Lemkul.
>
> I am facing a problem wherein the protein simulation is exploding only in
> this version - Gromacs-v5.0.5 but not in the older version Gromacs-v4.5.4.
>
> The warning message is as follows
>
> -------------------------------------------------------
> There were 4 inconsistent shifts. Check your topology
>
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+03
>     Number of steps    =        50000
>
> WARNING: Listed nonbonded interaction between particles 1312 and 1315
> at distance 4.728 which is larger than the table limit 2.000 nm.
>
> This is likely either a 1,4 interaction, or a listed interaction inside
> a smaller molecule you are decoupling during a free energy calculation.
> Since interactions at distances beyond the table cannot be computed,
> they are skipped until they are inside the table limit again. You will
> only see this message once, even if it occurs for several interactions.
>
> IMPORTANT: This should not happen in a stable simulation, so there is
> probably something wrong with your system. Only change the table-extension
> distance in the mdp file if you are really sure that is the reason.
> --------------------------------------------------------
> ATOM   1312  O   TYR A 207
> ATOM   1315  CD1 TYR A 207
> ---------------------------------------------------------
>
>
>
> -------------------------------------------------------------------
> em_real.mdp file
>
> ; LINES STARTING WITH ';' ARE COMMENTS
> title = Minimization ; Title of run
>
> ; 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 < 10.0 kJ/mol
> emstep      = 0.01      ; Energy step size
> nsteps = 50000   ; Maximum number of (minimization) steps to perform
> energygrps = Protein ; Which energy group(s) to write to disk
>
> ; 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
> cutoff-scheme   = Verlet
> 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 ; long range electrostatic cut-off
> rvdw    = 1.0 ; long range Van der Waals cut-off
> pbc        = xyz ; Periodic Boundary Conditions
>
>
> ------------------------------------------------------------------------
>
> The initial minimization step itself fails.

If minimization fails, you have a problem with the topology or coordinates. 
Perhaps you got a bit lucky with some quirk of an algorithmic difference in the 
old version that is failing here.

-Justin

> I have tried to simulate a minimized structure as well, I still encounter
> the same problem.
>
> I would appreciate any help in this regard.
> I would also like to know if this means, that the results from the older
> version of gromacs reliable?
>
> Thanking you in anticipation
>
> Nisha
>

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

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

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