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

Wed Dec 16 18:54:50 CET 2015

Dear Justin,

You are right and I totally agree with you. But, the point that I was
trying to make was that "the same input coordinates and input .mdp files
run in 4.5.4 and fail in 5.0.5".  Also, if this situation persists, does
that mean the results that have been obtained from the version 4.5.4 are
not reliable?

The second query was that - the topology and co-ordinates should be fine
because I have obtained these files from the simulation of protein alone in
version-5.0.5. Yet, I get LINCS warning for the protein atoms alone when I
simulate it as a complex with the ligand.
Kindly help me identify the problem.

Thanking you,
Nisha

On Wed, Dec 16, 2015 at 7:05 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/16/15 12:08 AM, NISHA Prakash wrote:
>
>> 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.
>>
>
> If the protein fails, you have a problem somewhere.  That's either
> topology (unlikely), coordinates (probable), or .mdp (most probable).  You
> said in your earlier message that energy minimization failed, which points
> to coordinates being the problem.
>
> 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.
>>
>>
> If you're comparing a protein-ligand complex in 5.0.5 against different
> complexes in 4.5.4, that is a meaningless comparison.  It's apples and
> oranges.  If the same input coordinates and input .mdp files run in 4.5.4
> and fail in 5.0.5, that might be something to look into.  But the general
> advice applies here - either way you're using outdated software, so if
> something is failing, upgrade to the latest version and try again.
>
> -Justin
>
>
> 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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> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
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