[gmx-users] Problem with lipid simulations

chris.neale at utoronto.ca chris.neale at utoronto.ca
Tue Apr 1 17:53:28 CEST 2008

Where is lipid.itp and your other forcefield files. Check that they  
are identical between your two clusters. This appears to be a problem  
with files and not with the installation. If you can't figure it out,  
you will need to post your topology at the very least and also post  
'grep LO ffoplsaa*.itp' or xxx in place of oplsaa for whatever ff you  
are using. That said, the error messages are pretty explicit. I assume  
that you checked to see that you are including atomtype LO, etc. more  
than once? You can probably figure out exactly where the problem is  
occurring by yourself and you are more likely to get some good advice  
ifyou do that.


-- original message --

Dear All,
I have been trying to simulate a small peptide in a DMPC lipid bylayer.
Same setup is working fine in one computer (cluster) but I am getting the
following error message in another cluster.
grompp_mpi -f test.mdp -c lipid_protein.gro -p topology.top -o test.tpr

checking input for internal consistency...
calling /lib/cpp...
processing topology...
WARNING 1 [file "lipid.itp", line 14]:
   Overriding atomtype LO
WARNING 2 [file "lipid.itp", line 15]:
   Overriding atomtype LOM
WARNING 3 [file "lipid.itp", line 16]:
   Overriding atomtype LNL
WARNING 4 [file "lipid.itp", line 17]:
   Overriding atomtype LC
WARNING 5 [file "lipid.itp", line 18]:
   Overriding atomtype LH1
WARNING 6 [file "lipid.itp", line 19]:
   Overriding atomtype LH2
WARNING 7 [file "lipid.itp", line 20]:
   Overriding atomtype LP
WARNING 8 [file "lipid.itp", line 21]:
   Overriding atomtype LOS
WARNING 9 [file "lipid.itp", line 22]:
   Overriding atomtype LP2
WARNING 10 [file "lipid.itp", line 23]:
   Overriding atomtype LP3
Cleaning up temporary file grompp16bicP
Program grompp_mpi, VERSION 3.3.1
Source code file: fatal.c, line: 416

Fatal error:
Too many warnings, grompp_mpi terminated

Please let me know how to get rid of this problem.

Thanks in advance


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