[gmx-users] Re: Mdrun error

[Justin A. Lemkul]

Cíntia C. Vequi-Suplicy wrote:
> Hello Justin,
> 
> I used Gromacs 4.0.5 and the error was gone. Thank you.
> 
> But now I have another problem when using mdrun_d. I gave the comand:
> 
> mdrun_d -s dppc.tpr -o dppc128.trr -c dppc128.gro -g dppc.log  &
> 
> And first I got  a lot of output on the shell window and I think it is 
> strange. This output should be on a file or not?
> And  after a few seconds I got an error which says:
> 
> t = 0.052 ps: Water molecule starting at atom 17276 can not be settled.
> Check for bad contacts and/or reduce the timestep.
> 
> Back Off! I just backed up step26b.pdb to ./#step26b.pdb.2#
> 
> Back Off! I just backed up step26c.pdb to ./#step26c.pdb.2#
> Wrote pdb files with previous and current coordinates
> MPI process rank 0 (n0, p23764) caught a SIGSEGV.
> 
> Can you help me?
> 

Your system is unstable and thus blowing up, due to any number of factors 
including incorrect force field parameters, inappropriate .mdp settings, 
insufficient minimization and/or equilibration, or any combination of the above.

Advice from the wiki:

http://oldwiki.gromacs.org/index.php/blowing_up

-Justin

> Thank you
> Cíntia C. Vequi-Suplicy
> Biophysics Group
> Physics Institute
> São Paulo University
> 
> Justin A. Lemkul wrote:
>>
>>
>> Cíntia C. Vequi-Suplicy wrote:
>>> Hello,
>>>
>>> I am trying to simulate a lipid membrane with Gromacs. I am trying to
>>> generate the *.tpr file o run the simulation, but every time I use the
>>> command grompp I got the following error:
>>>
>>> checking input for internal consistency...
>>> ...ling /usr/bin/cpp
>>> : No such file or directory
>>> cpp exit code: 32512
>>> dppc128.top > gromppzJXISa'cpp
>>> ' command is defined in the .mdp file
>>> *************************************************************
>>> * Important: if you do not have a c-preprocessor installed, *
>>> * you MUST run grompp with the "-pp" command line option    *
>>> * in place of the "-p" option.                              *
>>> *************************************************************
>>> processing topology...
>>> processing coordinates...
>>>
>>> -------------------------------------------------------
>>> Program grompp, VERSION 3.3.3
>>> Source code file: ../../../../src/kernel/grompp.c, line: 469
>>>
>>> Fatal error:
>>> number of coordinates in coordinate file (dppc128.gro, 17365)
>>>            does not match topology (dppc128.top, 0)
>>> -------------------------------------------------------
>>>
>>> "One Cross Each" (Monty Python)
>>>
>>> I don´t where the problem is, I've already checked the cpp compiler and
>>> it installed in the /usr/bin/cpp, as I put in the .mdp file. In the
>>> topology file I have the following lines:
>>>
>>
>> Have you tried the advice from grompp to use -pp instead of -p?
>>
>> General advice for this problem can be found here:
>>
>> http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology 
>>
>>
>> Also an option is to upgrade to the most recent version of Gromacs 
>> (4.0.5), which does not require cpp.
>>
>> -Justin
>>
>>> ;
>>> ;    File 'dppc128.top' was generated
>>> ;    By user: onbekend (0)
>>> ;    On host: onbekend
>>> ;    At date: Tue Aug 18 10:02:52 2009
>>> ;
>>> ;    This is your topology file
>>> ;    Pure DPPC bilayer with 128 lipids and 3655 water molecules
>>> ;
>>> ; The force field files to be include
>>> #include "ffoplsaa.itp"
>>> ; Include DPPC topology
>>> #include "dppc.itp"
>>> #include "lipid.itp"
>>> #include "spc.itp"
>>>
>>> [ molecules ]
>>> ; Compound   #mol
>>> DPP          128
>>> SOL          3655
>>>
>>> If anyone can help It will be very nice,
>>>
>>> Thank you very much so far,
>>> Cíntia C. Vequi-Suplicy
>>> Biophysics Group
>>> Physics Institute
>>> São Paulo University
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>>
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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