Thanks Christoph. Your responses are very fruitful. Finally, I am able to incorporated the tabulated dihedrals for CG simulations.
On a side note: One be very cautious while dealing with the tab. pot. For dihedrals, I used linear function to extrapolate the smoothed potentials. And of-course, always use whole (pbc whole) configurations. Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Fri, Oct 18, 2013 at 4:46 AM, Christoph Junghans <[email protected]>wrote: > 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. > -- 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.
