Re: [votca] Re: initial CG configuration

2016-08-31 16:15 GMT-06:00 Chang Woon Jang : > Dear Christoph, > > I re-extrapolated ABA angle (table_a1.xvg). The initial distribution > of ABA angle from BI is in Figure 1. After doing "csg_call --options > options.xml --ia-type angle --ia-name angle

Re: [votca] Re: initial CG configuration

Dear Christoph, I re-extrapolated ABA angle (table_a1.xvg). The initial distribution of ABA angle from BI is in Figure 1. After doing "csg_call --options options.xml --ia-type angle --ia-name angle --sloppy-tables convert_potential gromacs input output", in the lower angle, the slope is

Re: [votca] Re: initial CG configuration

2016-08-31 14:51 GMT-06:00 Chang Woon Jang : > Dear Christoph, > >It is zero at 180 degree. As you see in the figure (ABAanglehis.png - > supposed to be table_a1.xvg), value is zero at 180 degree. > > What I did, I removed the distribution below 1.5, then it is

Re: [votca] Re: initial CG configuration

Dear Christoph, It is zero at 180 degree. As you see in the figure (ABAanglehis.png - supposed to be table_a1.xvg), value is zero at 180 degree. What I did, I removed the distribution below 1.5, then it is extrapolated. Is this maybe the cause of failure of the run? Do I need to redo

Re: [votca] Re: initial CG configuration

Dear Christoph, When I change only harmonic angle from tabulated angle for "TDM" molecule in topology file (topol.top) as follow, it smoothly now works. The rest of bond, angle, dihedral still usethe tabulated (8) potentials. What does this mean? Is The tabulated angle potential derived

Re: [votca] Re: initial CG configuration

2016-08-31 9:25 GMT-06:00 Chang Woon Jang : > Dear Christoph, > > IBI still fails few iteration later the angle is going and coming at the > boundary. See the figures. I am not sure why GROMACS does not consider the > PBC effect. The 201-202-203 angle looks like over

Re: [votca] Re: initial CG configuration

2016-08-31 8:43 GMT-06:00 Chang Woon Jang : > Dear Votca Users, > >I have missed the figures. Figure 1 is initial configuration. Figure 2 is > the final iteration (1000 iteration) right before the ibi fails. > > Thank you. > > Best regards, > Changwoon Jang > > > On