[gmx-users] simulation error

Justin Lemkul jalemkul at vt.edu
Tue Sep 18 17:58:38 CEST 2018 


On 9/18/18 11:55 AM, Mario Andres Rodriguez Pineda wrote:
> when i try to run mdrun they start showing this:
> Steepest Descents:
>     Tolerance (Fmax)   =  1.00000e+03
>     Number of steps    =        50000
> Step=    0, Dmax= 1.0e-02 nm, Epot= -2.46652e+06 Fmax= 6.62812e+05, atom=
> 2881
> Step=    1, Dmax= 1.0e-02 nm, Epot= -2.48761e+06 Fmax= 6.51531e+05, atom=
> 2881
> Step=    2, Dmax= 1.2e-02 nm, Epot= -2.51019e+06 Fmax= 6.38455e+05, atom=
> 2881
> Step=    3, Dmax= 1.4e-02 nm, Epot= -2.53494e+06 Fmax= 6.23418e+05, atom=
> 2881
> Step=    4, Dmax= 1.7e-02 nm, Epot= -2.56238e+06 Fmax= 6.06180e+05, atom=
> 2881
> Step=    5, Dmax= 2.1e-02 nm, Epot= -2.59295e+06 Fmax= 5.86164e+05, atom=
> 2881
> Step=    6, Dmax= 2.5e-02 nm, Epot= -2.62704e+06 Fmax= 5.62063e+05, atom=
> 2881
> Step=    7, Dmax= 3.0e-02 nm, Epot= -2.66494e+06 Fmax= 5.31531e+05, atom=
> 2881
> Step=    8, Dmax= 3.6e-02 nm, Epot= -2.70684e+06 Fmax= 4.91124e+05, atom=
> 2881
> Step=    9, Dmax= 4.3e-02 nm, Epot= -2.75366e+06 Fmax= 4.36752e+05, atom=
> 2881
> Step=   10, Dmax= 5.2e-02 nm, Epot= -2.80104e+06 Fmax= 3.67647e+05, atom=
> 2881
> Step=   11, Dmax= 6.2e-02 nm, Epot= -2.84787e+06 Fmax= 4.16988e+05, atom=
> 2883
> Step=   12, Dmax= 7.4e-02 nm, Epot= -2.86654e+06 Fmax= 2.20175e+06, atom=
> 2903
> Step=   13, Dmax= 8.9e-02 nm, Epot= -2.88894e+06 Fmax= 2.80767e+05, atom=
> 2883
> Step=   14, Dmax= 1.1e-01 nm, Epot= -2.95328e+06 Fmax= 1.33061e+05, atom=
> 2883
> Step=   15, Dmax= 1.3e-01 nm, Epot= -3.03044e+06 Fmax= 2.52114e+05, atom=
> 2881
>
> step 16: One or more water molecules can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> tMPI error: Receive buffer size too small for transmission (in valid comm)
> Abort (core dumped)
>
> I don't understand what happend. Please can you help me? How i can reduce
> timestep?

You're stuck at a huge force on atom 2881. Check on what that is, what's 
around it, etc.

If necessary, you can reduce emstep (energy minimization step size, not 
dt which is the time step in MD) to a smaller value. I don't think 
that's going to be an effective fix here. EM is clearly stuck trying to 
resolve something bad in your structure and it can't do it.

-Justin

> Em ter, 18 de set de 2018 às 08:36, Justin Lemkul <jalemkul at vt.edu>
> escreveu:
>
>>
>> On 9/18/18 12:42 AM, Mario Andres Rodriguez Pineda wrote:
>>> These were the errors until the moment of executing the minimization:
>>>
>>> After adding ions grompp:
>>> NOTE 1 [file topol.top, line 37566]:
>>>     System has non-zero total charge: -18.999999
>>>     Total charge should normally be an integer. See
>>>     http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>>>     for discussion on how close it should be to an integer.
>>>
>>> minimization mdrun
>>> step 16: One or more water molecules can not be settled.
>>> Check for bad contacts and/or reduce the timestep if appropriate.
>>> Wrote pdb files with previous and current coordinates
>>> tMPI error: Receive buffer size too small for transmission (in valid
>> comm)
>>> Abort (core dumped)
>>>
>>> In attach send you the mdp archive for minimization run.
>> The mailing list does not allow attachments.
>>
>> Use the -v flag of mdrun to track the energy and forces at every step
>> until the crash to see what's going on and where the maximum force is
>> acting. There's probably a bad contact somewhere that can't be relaxed
>> and you need to investigate why that's happening.
>>
>> -Justin
>>
>>> Thanks for your help
>>>
>>> Em seg, 17 de set de 2018 às 19:56, Justin Lemkul <jalemkul at vt.edu>
>>> escreveu:
>>>
>>>> On 9/17/18 6:47 PM, Mario Andres Rodriguez Pineda wrote:
>>>>> Hi everyone.
>>>>> I'm trying simulate a protein in water followin lysozyme tutorial using
>>>>> gromacs 2016.3. When triying minimize the system after make the box and
>>>>> insert a salt concentration the minimization has been stoped sendingme
>>>> the
>>>>> following error:
>>>>>
>>>>> step 16: One or more water molecules can not be settled.
>>>>> Check for bad contacts and/or reduce the timestep if appropriate.
>>>>> Wrote pdb files with previous and current coordinates
>>>>> tMPI error: Receive buffer size too small for transmission (in valid
>>>> comm)
>>>>> Abort (core dumped)
>>>> Water SETTLE problems are not unusual in energy minimization and are
>>>> often resolved. If, however, such a message immediately precedes a
>>>> failure, then you have a serious problem with either the coordinates or
>>>> topology. mdrun prints out which atom is experiencing the maximum force,
>>>> so start by looking there, as well as reviewing your notes about what
>>>> warnings pdb2gmx or grompp may have issued (but surely you wouldn't have
>>>> ignored any, right? :).
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> Justin A. Lemkul, Ph.D.
>>>> Assistant Professor
>>>> Virginia Tech Department of Biochemistry
>>>>
>>>> 303 Engel Hall
>>>> 340 West Campus Dr.
>>>> Blacksburg, VA 24061
>>>>
>>>> jalemkul at vt.edu | (540) 231-3129
>>>> http://www.thelemkullab.com
>>>>
>>>> ==================================================
>>>>
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>>>
>>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>
>

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

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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

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