2014/1/4 xiaowu759 <[email protected]>: > Dear VOTCA's users, > I try to obtain the bonded CG potentials using the IBI method, which is > implemented in the VOTCA-1.3-dev. The target distributions are produced by > running csg_stat. While running csg_inverse, the errors always come up, as > given below. From these error messages, I guess that there are some > disadvantages in the obtained CG potentials. How to deal with this problem, > please? To get a detailed help, I upload all the files involved. I didn't had a look at your input yet, but here are a couple of general tricks: - start from an simple case and add it more stuff later - use simple Boltzmann inverted bonded potentials and make the iteration of the non-bonded iteration work first, then add in the iteration of the bonded one. - have a look at step_XXX/*.pot.cur to see what kind of potential VOTCA generates from your target distribution, maybe you will have to play with min/max of each interaction. Also have a look at step_XXX/*.xvg to see if the conversion from *.pot.cur worked.
Concerning your error message there might be a couple of causes: - system exploded for various reasons (wrong potential, wrong initial condition), have a look at the simulation movie with VMD - table is too short, increase table_end (but don't increase max) - forgotten interactions, your table.xvg is full of zeros, so every pairs, which is not listed in energygrp_table in your mdp file will not interact at all. (energygrp_table is empty in your mdp file, are you doing a vacuum simulation? If so simple BI should be enough.) Cheers, Christoph > Best regards, > Chaofu Wu > > conf.gro <http://votca.966470.n3.nabble.com/file/n4024628/conf.gro> > index.ndx <http://votca.966470.n3.nabble.com/file/n4024628/index.ndx> > grompp.mdp <http://votca.966470.n3.nabble.com/file/n4024628/grompp.mdp> > topol.top <http://votca.966470.n3.nabble.com/file/n4024628/topol.top> > settings.xml <http://votca.966470.n3.nabble.com/file/n4024628/settings.xml> > cg_map.xml <http://votca.966470.n3.nabble.com/file/n4024628/cg_map.xml> > table.xvg <http://votca.966470.n3.nabble.com/file/n4024628/table.xvg> > bond_AA.dist.tgt > <http://votca.966470.n3.nabble.com/file/n4024628/bond_AA.dist.tgt> > bond_AB.dist.tgt > <http://votca.966470.n3.nabble.com/file/n4024628/bond_AB.dist.tgt> > angle_AAA.dist.tgt > <http://votca.966470.n3.nabble.com/file/n4024628/angle_AAA.dist.tgt> > angle_AAB.dist.tgt > <http://votca.966470.n3.nabble.com/file/n4024628/angle_AAB.dist.tgt> > dihedral_AAAA.dist.tgt > <http://votca.966470.n3.nabble.com/file/n4024628/dihedral_AAAA.dist.tgt> > dihedral_AAAB.dist.tgt > <http://votca.966470.n3.nabble.com/file/n4024628/dihedral_AAAB.dist.tgt> > dihedral_BAAB.dist.tgt > <http://votca.966470.n3.nabble.com/file/n4024628/dihedral_BAAB.dist.tgt> > > ################################################################################ > # > # > # ERROR: > # > # critical: 'mdrun -s topol.tpr -c confout.gro -o traj.trr -x traj.xtc' > failed # > # For details see the logfile /home/xiaowu759/Workshop/inverse.log > # > # > # > ################################################################################ > The inverse.log file gives a more detail > Fatal error: > A tabulated bond interaction table number 1 is out of the table range: r > 2.528434, between table indices 2528 and 2529, table length 2501 > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > > > > > -- > View this message in context: > http://votca.966470.n3.nabble.com/How-to-deal-with-the-problem-during-the-IBI-procedure-for-the-bonded-parts-tp4024628.html > Sent from the votca mailing list archive at Nabble.com. > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/groups/opt_out. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
