2013/10/14 Chandan Choudhury <[email protected]>: > > Dear votca users, > > I intend to use the dihedral tabulated potentials. I have generated the > distributions and potentials from csg_boltzmann. Then I use the following > commands to generate the tab. potentials. > > Here smoothing is necessary as the potential is noisy. I use the quadratic > extrapolation. > > source /opt/apps/gmx/single/463/bin/GMXRC > GMXLIB=/opt/apps/gmx/single/463/share/gromacs/top > source /opt/apps/votca/1.2.3/bin/VOTCARC.bash > > sed -e '1,2d' -e 's/$/ i/' $1.dihedral.pot | tac | sed -e '1,1d' | tac > > $1.dihedral.cut > csg_call table smooth $1.dihedral.cut $1.dihedral.smooth > csg_resample --in $1.dihedral.smooth --out $1.dihedral.refined --grid > -3.141::0.001:3.141 > csg_call table extrapolate --function quadratic $1.dihedral.refined > $1.dihedral.ep > awk '{print $1/3.141592654*180.0,$2}' $1.dihedral.ep > $1.dihedral.pot.cur > csg_call --ia-type dihedral --ia-name $1.dihedral --options convert.xml > convert_potential gromacs > > The tabulated potentials are used for the dihedrals. On using these > potentials, I get the errors (Please see attached log file). These error > also pops when I use -nt=1. > > When I fit a RB potential function to the dihedrals (smoothed potential) and > use the function type 3 for it, the simulation proceeds. > Also, when I switch off the dihedrals (by commenting the topol.top), the > simulation executes without any problem. > > I have also attached the topology and the structure file for the reference. > > Does anyone has encounter this type of problem. Is there some way to tackle > dihedrals. Any insight would be very fruitful. Either your table isn't long enough or the system is exploding in the 1st step. Make sure your conf.gro has correct pbc, running trjconv -pbc mol might help. Or try to minimize with some harmonic potentials first.
Cheers, Christoph > > Chandan > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > -- > 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.
