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
--
______________________________________________
Anna Marabotti, Ph.D.
Assistant Professor
Department of Chemistry and Biology
University of Salerno
Via Giovanni Paolo II, 132
84084 Fisciano (SA)
Italy
Phone: +39 089 969583
Fax: +39 089 969603
E-mail: amarabo...@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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