[gmx-users] still dealing with GFP-like chromophore with LINCS warnings

Baptiste Demoulin bat.demoulin at gmail.com
Thu Jun 27 18:17:59 CEST 2013

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...


2013/6/27 Anna Marabotti <amarabotti at 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 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
> --
> ______________________________**________________
> 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: amarabotti at unisa.it
> Skype: annam1972
> Web page: http://www.unisa.it/docenti/**annamarabotti/index<http://www.unisa.it/docenti/annamarabotti/index>
> "Indifference is the eighth deadly sin" (don Andrea Gallo)
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>

More information about the gromacs.org_gmx-users mailing list