Re: [votca] force constant in tabulated bond, angle, and dihedral

2016-08-30 18:48 GMT-06:00 Chang Woon Jang : > Dear Votca Users, > > > I would like to know how to determine force constants for topol.top > from all tutorials. All the force constants k set 1.0. What is the criteria > for selecting the force constants? The potentials

[votca] force constant in tabulated bond, angle, and dihedral

Dear Votca Users, I would like to know how to determine force constants for topol.top from all tutorials. All the force constants k set 1.0. What is the criteria for selecting the force constants? Since the force constants are already listed in tabulated table in third column, can you

Re: [votca] warning

2016-08-30 13:18 GMT-06:00 Chang Woon Jang : > Dear Christoph, > > I think that bond potentials seem to be good with U shape using > csg_call --options options.xml --ia-type bond --ia-name bond > convert_potential gromacs Yeah, the attached bond potentials actually

Re: [votca] warning

Dear Christoph, I think that bond potentials seem to be good with U shape using csg_call --options options.xml --ia-type bond --ia-name bond convert_potential gromacs The following potentials in figures are obtained from csg_call. I am not sure of forces though. With all those

Re: [votca] warning

2016-08-30 12:33 GMT-06:00 Chang Woon Jang : > Dear Christoph, > >It runs smoothly up to 12500 iterations. After that the error still exist > as follows. Luckily, 10K iterations do not produce the error. The below error means a bond got stretched more than 2.02391 nm,

Re: [votca] warning

2016-08-30 12:22 GMT-06:00 Chang Woon Jang : > Dear Christoph, > >Did you also change original bond and angle tables to gromacs format? I only looked at the dihedral! > > If so, how do I determine the min and max values for bond and angle tables? Basically you look at

Re: [votca] warning

Dear Christoph, It runs smoothly up to 12500 iterations. After that the error still exist as follows. Luckily, 10K iterations do not produce the error. DD step 12499 load imb.: force 5.6% Step Time Lambda 125006.250000.0

Re: [votca] warning

Hi, thanks for sending the potentials. Here is what I did: $ ls table_d*.txt table_d1.txt table_d2.txt table_d3.txt table_d4.txt # These are the potentials out of csg_boltzmann $ cat table_d.xml dihedral -3.141 3.141 0.001 1e8 0.001 $

Re: [votca] how to convert dihedral potential from csg_boltzmann to gromacs potential

2016-08-29 14:47 GMT-06:00 Christoph Junghans : > 2016-08-29 14:37 GMT-06:00 Chang Woon Jang : >> Dear Christoph, >> >> >> What I have used is the following command with the options.xml file. >> >> >> >> >> >> dihedral >> 0.285 >>