[gmx-users] how to deal with LINCS warnings despite prolonged stabilization of the system?

Anna Marabotti amarabotti at unisa.it
Wed Jul 3 10:52:02 CEST 2013

Dear all,
I'm writing again because I really need to understand what more can I do 
on my systems that are still dealing with LINCS warnings. I minimized 
further the systems (from emtol 500 to emtol 100) and the final 
potential energies and max force were nearly identical to those I 
obtained when emtol was set to 500, in my opinion this indicates that 
the system has already converged to a minimum. I made a NVT (thermostat: 
V-rescale) for 100 ps and a NPT (thermostat: V-rescale and barostat: 
Berendsen) for 1 ns, and I checked the energies of the system: all was 
regular without any apparent perturbation. I then started the production 
run in NPT ensemble (thermostat: V-rescale and barostat: 
Parrinello-Rahman or Berendsen - I tried both of them) and approx. after 
10-15 ns my system turns on LINCS WARNINGS (but never at the same time), 
and sometimes produces many stepXXXXX.pdb files, stopping the 
simulation. When I look at the energies of the system, I don't see 
anything strange apart the fact that the graph is interrupted. When I 
see the simulations with VMD, I don't see anything strange apart some 
crossings of the periodic boundaries (I don't see any system "exploding" 
or so on). I have the doubt that the cofactor could be badly 
parameterized, but LINCS WARNINGS do not involve only the cofactor, but 
also the protein backbone (the cofactor is covalently bound to protein 
backbone, but LINCS WARNINGS do not involve the parts of protein 
directly bound to the cofactor: would it be possible such an effect when 
only the cofactor is badly parameterized?)
Please give me some suggestions. I read documentation in GROMACS web 
site, but I did all I saw, apart for skipping LINCS WARNING, including 
the analysis of the g_energy terms and comparison with the simulations 
that went well. I don't see any significant difference (if somebody 
wants to see, I can provide the files)

Thanks a lot

Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via Giovanni Paolo II, 132
84084 Fisciano (SA)
Phone: +39 089 969583
Fax: +39 089 969603
E-mail: amarabotti at unisa.it
Skype: annam1972
Web page: http://www.unisa.it/docenti/annamarabotti/index

"Indifference is the eighth deadly sin" (don Andrea Gallo)

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