Hello Christoph, Sorry for the incessant questioning.
I got the point that csg_inverse will do the extension automatically. But when I am using Boltzmann Inversion (not IBI) to get the bonded potential, then do I need to do the modifications (extending the range of the potential) manually by using the post-processing tools in VOTCA? Or can I use csg_inverse for simple Boltzmann Inversion also? Thank you. Sanjeet On Wednesday, October 19, 2022 at 12:17:04 PM UTC-4 Christoph Junghans wrote: > On Wed, Oct 19, 2022 at 9:24 AM Sanjeet Singh <[email protected]> wrote: > > > > Dear Christoph, > > > > I would like to ask a follow-up question to this. Now, suppose I set my > min = 0.351 and max = 0.367, then I will be getting my potential in this > range. What if I want to extend my potential outside this range, Say for > example the range of my dist.tgt file. The range of my dist.tgt file is > 0.347465 to 0.371461. It's just that in the boundary regions of dist.tgt > file I don't have a proper sampling. > > csg_inverse would to the extension automatically, for manually > modification see: > > https://www.votca.org/csg/preparing.html?highlight=extrapolate#post-processing-of-the-potential > > Christoph > > > > On Wednesday, October 19, 2022 at 9:05:53 AM UTC-4 Christoph Junghans > wrote: > >> > >> On Tue, Oct 18, 2022 at 6:30 PM Sanjeet Singh <[email protected]> > wrote: > >> > > >> > Hello Christoph, > >> > > >> > Thank you for your prompt response. But, I am not able to follow you > when you say "for csg_botlzmann it doesn't really matter". > >> What I meant there was that csg_boltzmann will invert things either > >> way, but what I would do is to pick min and max inside the peak of the > >> distribution, so 0.351 and 0.367, as you suggested, should work. > >> > >> Christoph > >> > >> > > >> > For example in my dist.tgt file here, I have initial data points as > follows: > >> > > >> > 0.347465 0.00833478 > >> > 0.347705 0.00833478 > >> > 0.347945 0.0166696 > >> > 0.348185 0 > >> > 0.348425 0.00833478 > >> > > >> > Therefore, when I am using this dist.tgt file to get bonded potential > using Boltzmann Inversion I am setting the min at 0.348425 as before this I > am having a point with zero probability. > >> > > >> > Or if I set my min at the starting point 0.347465, then will this be > OK? > >> > > >> > > >> > On Tuesday, October 18, 2022 at 6:30:42 PM UTC-4 Christoph Junghans > wrote: > >> >> > >> >> On Tue, Oct 18, 2022 at 12:43 PM Sanjeet Singh <[email protected]> > wrote: > >> >> > > >> >> > Hello Christoph, > >> >> > > >> >> > I have run a 1000 ns atomistic vacuum simulation to get bonded > distribution with exclusions obtained using the following command: > >> >> > > >> >> > csg_boltzmann --top topology.xml --cg mapping.xml --excl > exclusions.txt > >> >> > > >> >> > Then, I am getting my bonded distribution using the following > command: > >> >> > > >> >> > csg_boltzmann --top topology.xml --trj Trajectory2.dump --cg > PEO-10.xml --first-frame 500000 < boltzmann_cmds_dist > >> >> > > >> >> > After getting my bonded distribution I want to use Boltzmann > Inversion to get my bonded potential using the following command: > >> >> > > >> >> > csg_boltzmann --top topology.xml --trj Trajectory2.dump --cg > PEO-10.xml --first-frame 500000 < boltzmann_cmds > >> >> > > >> >> > Now, suppose I want to do the Boltzmann Inversion for a Bond-AB > for which I am using the boltzmann_cmds file with the following options: > >> >> > > >> >> > tab set T 300 > >> >> > tab set scale bond #SCALING IS NEEDED TO GET THE VOLUME NORMALIZED > DISTRIBUTION FUNCTION i.e. dividing the distribution by 4pir^2 > >> >> > tab set auto 0 > >> >> > tab set min ______ > >> >> > tab set max _____ > >> >> > tab set n 100 > >> >> > tab bond-AB.potential-file-100.ib *bond-AB* > >> >> > > >> >> > Then in the above lines, what should be the value of min and max? > >> >> > > >> >> > I am attaching the bonded distribution file for BOND-AB here, and > also the plot of BOND-AB distribution. > >> >> > > >> >> > If I go by the BOND-AB distribution file, then maybe I can use min > = 0.348425, and max = 0.369061. As before this min and after the max value, > I have 0 probability for some bond length. > >> >> > > >> >> > Or, should I select min and max from the plot of the distribution? > And select min = 0.351, and max = 0.367, i.e. the range where I have the > normal distribution in the plot. > >> >> Short answer is for csg_botlzmann it doesn't really matter. > >> >> However, for csg_inverse the min and max matter, so the boltzmann > >> >> inversion from the target distribution (<name>.dist.tgt) is done > >> >> correctly, if you don't provide an initial guess for the potential > >> >> (<name>.pot.in) > >> >> > >> >> Christoph > >> >> > >> >> > > >> >> > Thank you. I would appreciate any advice you have for me. > >> >> > > >> >> > > >> >> > -- > >> >> > Join us on Slack: https://join.slack.com/t/votca/signup > >> >> > --- > >> >> > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/6187e55a-2925-4a5c-992e-8f3c44112b1bn%40googlegroups.com > . > >> >> > >> >> > >> >> > >> >> -- > >> >> Christoph Junghans > >> >> Web: http://www.compphys.de > >> > > >> > -- > >> > Join us on Slack: https://join.slack.com/t/votca/signup > >> > --- > >> > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/60ada3ad-6d4f-473c-91ca-1a703f12891en%40googlegroups.com > . > >> > >> > >> > >> -- > >> Christoph Junghans > >> Web: http://www.compphys.de > > > > -- > > Join us on Slack: https://join.slack.com/t/votca/signup > > --- > > 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 view this discussion on the web visit > https://groups.google.com/d/msgid/votca/86dd6512-6372-4061-a1d8-130f429ebc6fn%40googlegroups.com > . > > > > -- > Christoph Junghans > Web: http://www.compphys.de > -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. 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