2017-06-05 21:22 GMT-06:00 M. Chakraborty <[email protected]>: > Hello, > > I have a few questions about getting potential tables from force-matching > and finally converting it to table.xvg format using table.xml. > > 1) The example table.xml in the votca manual (Chapter 4) has the details of > the required table.xvg file within the <inverse>....</inverse> block. If I > am not mistaken, that is used for boltzmann inversion. I tried writing the > same table information under <fmatch> . . . </fmatch> block but it does not > work. So, even when I am using force-matching, can I have an <inverse> . . > .</inverse> block under each interaction specifying the details of the > table.xvg file? No, force-matching is a non-iterative method, just follow section 4.3 of the manual first and then follow section 4.2. And yes, most information needs to go into the <inverse>....</inverse> block as csg_call makes use of the potential post-processing scripts from boltzmann inversion.
> > 2) The manual says using the "convert_potential gromacs" tag with csg_call > will automatically resample the potential from 0, extrapolate to the end of > the table on the right and extrapolate the potential on left for 0 distance. > Does that mean, we can skip the resampling and extrapolation step prior to > the csg_call step ? I would like to mention that when I had my potential > tables starting from non-zero value and tried to use csg_call, I got an > error saying that the potential table should start from 0. It depends "convert_potential gromacs" will do all things listed at the end of section 4.2.4. However, sometimes you need to prepare the potential somehow first, e.g. - throwing away under sampled regions - clean up values at the boundaries etc. And that is what sections 4.2.1 to 4.2.3 talk about. >From my own experience, you first want to prepare and convert a couple of potential by hand, before fully trusting "convert_potential gromacs". Christoph > > Thanks. > > M. Chakraborty > > -- > 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 https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- 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 https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
