In fact in the reverse transformation I'm feeding the CG structure information. Once I look through VMD to the FG structure I notice that the backbones are not in planes so definitely I need to run some minimization there. In the tutorial they were using simulating annealing, but I don't think I need more than energy minimization for that. What do you think?
2012/2/10 Mark Abraham <mark.abra...@anu.edu.au> > On 11/02/2012 12:41 AM, francesca vitalini wrote: > > In order to overcome the problem I tried to fix everything except the > backbone (solvent, sidechain and CA, as I want the structure to be > maintained). However, if I do then I have problems with the energy > minimization as the force on the 15300 is infinite. > > Getting Loaded... > Reading file EM1-1.tpr, VERSION 3.3.1 (single precision) > Loaded with Money > > Steepest Descents: > Tolerance (Fmax) = 1.00000e+01 > Number of steps = 2000 > ------------------------------------------------------- inf, atom= > 15300 > Program mdrun, VERSION 3.3.1 > Source code file: nsgrid.c, line: 226 > > Range checking error: > Explanation: During neighborsearching, we assign each particle to a grid > based on its coordinates. If your system contains collisions or parameter > errors that give particles very high velocities you might end up with some > coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot > put these on a grid, so this is usually where we detect those errors. > Make sure your system is properly energy-minimized and that the potential > energy seems reasonable before trying again. > > Variable ci has value -2147483648. It should have been within [ 0 .. > 27744 ] > Please report this to the mailing list (gmx-users@gromacs.org) > ------------------------------------------------------- > > "Oh My God ! It's the Funky Shit" (Beastie Boys) > > Halting program mdrun > > You suggested to check if there is any overlapping. > > > ... so you need to get out some visualization software and look at the > transformed structure :) > > > There might be as my structure is obtained through a reverse > transformation from a CG representation. In the mapping the atoms are > positioned randomly in the bead. Now I'm running some energy minimization > to equilibrate those atoms. I had to solvate the system after the mapping > (couldn't do it before due to problems with ions)but I haven't equilibrated > it yet and I'm keeping it fixed which could also be a source of > overlapping. > > > Local minimization with EM cannot in general take a "random" positioning > of the generated atoms and make it one that will be stable under MD. Some > structure knowledge needs to be build into the reverse transformation. > > Mark > > > Any ideas? > Thanks. > Francesca > > > 2012/2/10 Justin A. Lemkul <jalem...@vt.edu> > >> >> >> francesca vitalini wrote: >> >>> I achieve >>> >>> Steepest Descents converged to machine precision in 205 steps, >>> but did not reach the requested Fmax < 10. >>> Potential Energy = -1.49131940478719e+07 >>> Maximum force = 1.09664530279637e+06 on atom 1520 (parto of the >>> protein) >>> Norm of force = 2.28369808518165e+06 >>> >>> >> The magnitude of the force suggests atomic overlap somewhere. Start by >> investigating the environment around atom 1520. >> >> >> and the system looked with vmd doesn't look as if it was exploding. >>> However, I have warnings about the table extension and I don't know why but >>> gromacs writes pdb files sometime. However I thought that there >>> >> >> The "step.pdb" files are written when mdrun is about to crash. >> >> >> might have been an error in the way I defined the position restraints, >>> in fact in the mdp file I hade define = -DEPOSRE while in the topology I >>> had ifdef DEFINE_WAT, so it might have moved it all without fixing the >>> water. So I tried again and this time I got >>> >>> >> The "define" statements are literal, so be careful of typos. -DEPOSRE >> will not work when the topology calls for -DPOSRES. So unless you've >> changed default naming for "define" statements, you're not going to get >> what you expect. >> >> >> Steepest Descents converged to machine precision in 72 steps, >>> but did not reach the requested Fmax < 10. >>> Potential Energy = -2.0135496e+07 >>> Maximum force = 2.0486184e+12 on atom 4479 >>> Norm of force = 7.2424045e+13 >>> >>> >> Again, symptomatic of severe atomic overlap. >> >> >> but again the same issue with table extent and still the production of >>> pdb files. >>> >>> Any explanations? >>> >>> >> Investigate the starting configurations near the problematic atoms. >> >> >> http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System >> >> -Justin >> >> >> -- >> ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- >> 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 >> > > > > -- > Francesca Vitalini > > PhD student at Computational Molecular Biology Group, > Department of Mathematics and Informatics, FU-Berlin > Arnimallee 6 14195 Berlin > > vital...@zedat.fu-berlin.de > francesca.vital...@fu-berlin.de > > +49 3083875776 > +49 3083875412 > > > > > > -- > 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 > -- Francesca Vitalini PhD student at Computational Molecular Biology Group, Department of Mathematics and Informatics, FU-Berlin Arnimallee 6 14195 Berlin vital...@zedat.fu-berlin.de francesca.vital...@fu-berlin.de +49 3083875776 +49 3083875412
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