Thanks a lot! On Tuesday, 6 June 2017 00:32:45 UTC-4, Christoph Junghans wrote: > > 2017-06-05 21:22 GMT-06:00 M. Chakraborty <[email protected] > <javascript:>>: > > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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 >
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