[gmx-users] Mdrun error

["Cíntia C. Vequi-Suplicy"]

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?

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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>