[gmx-users] still dealing with GFP-like chromophore with LINCS warnings
amarabotti at unisa.it
Thu Jun 27 15:47:36 CEST 2013
I'm still dealing with the problem of GFP-like chromophore. To be
honest, with the help of another gmx user, I was able to obtain the
topology of my chromophore, in protonated and unprotonated form, and I
started performing the simulations. For the protonated chromophore, all
worked well, and I obtained my simulations without many problems.
Instead, I'm experimenting problems with the protein containing the
unprotonated form. In particular, when I started calculating the
production run, using in the .mdp files exactly the same parameters used
for the protonated form, I started obtaining a lot of LINCS warnings and
production of a lot of stepXXXXX.pdb files. This happened only during
the production run, whereas I have no errors during minimization and
position-restrained dynamics. The minimization step seems to be OK and I
did not further continue with it (I set emtol=500 and emstep=0.01; the
result of minimization was:
Steepest Descents converged to Fmax < 500 in 2114 steps
Potential Energy= -6.84833590617959e+05
Maximum force=4.57025361763790e+02 on atom 2129
Norm of force=9.42624640937790e+00
that seems pretty good for me.)
I tried to overcome the problem by using longer PR-MD (100 ps instead of
10 for NVT; 1 ns instead of 100 ps for NPT) but it doesn't work, despite
the fact that the energies and all other factors (temperature, pressure)
are really stable during PR-MD. I also watched the trajectory using VMD
but, apart from parts of protein crossing periodic boundaries (a thing
that I see regularly in my simulations), I don't see anything "strange"
(like system exploding). Apparently, it simply stops, and that's all.
Other things that trouble me are:
1) I checked the atoms with LINCS warning, and I see that not only those
atoms belonging to chromophore are perturbed, but also other atoms in
the backbone of the protein (mainly CA-C-N; many of them, but not all,
are spatially close to chromophore).
2) during these production runs I also experimented many hardware
problems (power outages) and software problems (bad job schedulation,
problems in core communications etc) and I don't understand if these
problems could affect the results of my simulation in this way. I ask
this because my first production run was stopped because of a power
outage, and in the .log file I saw a lot of errors very early; when the
machine turned on, I resent exactly the same dynamics, and the errors
were far later than before (in the first run, they came across 5 ns; in
the second run not before 20 ns).
3) Last thing: when I started the production run, I switched the
pressure coupling from Berendsen to Parrinello-Rahman (obviously not
giving the .edr file to grompp for the creation of the full.tpr file)
(on the contrary, the temperature coupling was left V-rescale both in
PR-Md and production run). Can this switch perturb the system?
My question is: do I have to suppose that the unprotonated form of
chromophore is badly parametrized, and this can influence all the rest
of the protein in this way? If yes, why nothing happens when I do PR-MD?
If not, do I have simply to perform a very very very long stabilization,
do I have to perform a deeper minimization, do I have to avoid switching
from Berendsen to Parrinello? What do you suggest me to do?
Thanks a lot
Anna Marabotti, Ph.D.
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
Web page: http://www.unisa.it/docenti/annamarabotti/index
"Indifference is the eighth deadly sin" (don Andrea Gallo)
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