I did experience some troubles using Parrinello-Rahman after an
equilibration with Berendsen. Trying many different time-constant was the
solution ( I had to shift this constant from 10 ps for Berendsen to 5 ps
for PR). Did you try to change it ? I do not know the fundamental reasons
for this problem, though...
Baptiste
2013/6/27 Anna Marabotti amarabo...@unisa.it
Dear gmx-users,
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 stepX.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
--
__**
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/indexhttp://www.unisa.it/docenti/annamarabotti/index
Indifference is the eighth deadly sin (don Andrea Gallo)
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