[gmx-users] simulation error

[Justin Lemkul]

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.

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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

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