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 ([email protected]) ------------------------------------------------------- "Oh My God ! It's the Funky Shit" (Beastie Boys) Halting program mdrun You suggested to check if there is any overlapping. 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. Any ideas? Thanks. Francesca 2012/2/10 Justin A. Lemkul <[email protected]> > > > 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<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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<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 [email protected] [email protected] +49 3083875776 +49 3083875412
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