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

[NISHA Prakash]

Dear Justin,

I am simulating a protein ligand complex. The protein co-ordinate file that
I have taken is an output of the simulation of the protein alone in
Gromacs-v5.0.5. The topology and the co-ordinates are fine. I am still
facing this problem wherein I get the LINCS warning for only the protein
atoms. The ligand also is fine.
Like I mentioned before, I do not have this problem when I use the
Gromacs-4.5.4 where I have used the same co-ordinate file with different
ligands and same parameter file.

Kindly let me know how to resolve the issue.

Thanking you in anticipation.

Nisha




On Wed, Dec 16, 2015 at 12:26 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
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