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 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: amarabo...@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@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-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
