On Thursday, April 12, 2018 at 4:55:47 PM UTC-4, Christoph Junghans wrote:
>
> On Thu, Apr 12, 2018 at 2:28 PM, Alexander Alexander 
> <alexand...@gmail.com <javascript:>> wrote: 
> > 
> > Thank you. 
> > 
> > An then these parameter 
> > <pot_max>10000000</pot_max> 
> > <table_end>4.0</table_end> 
> > which usually comes in the very end of settings.xml of IBI in the 
> <inverse> 
> > section, are again mx of potential and end of it, which should be larger 
> > than all our end table in each section. 
> Like I said, these are parameter for the gromacs table (the xvg file), 
> not the VOTCA table (the pot.new file). 
> You could set them differently for each table, but usually the values 
> above should work for most Gromacs runs. 
>
> > 
> > On Thursday, April 12, 2018 at 4:09:27 PM UTC-4, Christoph Junghans 
> wrote: 
> >> 
> >> On Thu, Apr 12, 2018 at 2:03 PM, Alexander Alexander 
> >> <alexand...@gmail.com> wrote: 
> >> > 
> >> > Hi Christoph, 
> >> > 
> >> > I guess I found out what do you mean, I hope the attached bonded 
> tables 
> >> > for 
> >> > 3-bead system would be fine. 
> >> Yeah these one look better, if you zoom around the minimum you should 
> >> see some structure for the Boltzmann inversion. 
> > 
> > 
> > Yes, when I zoom in them, I see a wide U shape for each of bonded 
> > interactions as in attachment. 
> > Now, to use them in IBI (only nonbonded), should I use the zoomed 
> version of 
> > them or these are fine for IBI over nonbonded? 
> If you are doing only non-bonded IBI, just provide VOTCA with the full 
> table_a1.xvg, table_b1.xvg etc. and add them to <filelist> as well. 
> Also don't forget to remove the <bonded> sections of the interactions 
> you aren't iterating from your settings.xml file. 
>
Probably I can even keep them in the setting but not updating them, I mean 
"<do_potential>0 0 0</do_potential>",  but improving them via below command 
just by smoothing and scaling them as below.
                <post_update>smooth</post_update>
                <post_update_options>
                <scale>0.001</scale>
                </post_update_options>
                <post_add>convergence</post_add>
 
How about if I want to do the full IBI (both bonded and nonbonded), using 
those table_a,b.xvg?

Regards,
Alex

>
> Christoph 
> > 
> > Thank you. 
> > Regards, 
> > Alex 
> >> 
> >> 
> >> Christoph 
> >> > 
> >> > Best regards, 
> >> > Alex 
> >> > 
> >> > 
> >> > On Thursday, April 12, 2018 at 1:26:37 PM UTC-4, Alexander Alexander 
> >> > wrote: 
> >> >> 
> >> >> 
> >> >> Thanks. 
> >> >> 
> >> >> On Thursday, April 12, 2018 at 12:43:54 PM UTC-4, Christoph Junghans 
> >> >> wrote: 
> >> >>> 
> >> >>> On Thu, Apr 12, 2018 at 9:57 AM, Alexander Alexander 
> >> >>> <alexand...@gmail.com> wrote: 
> >> >>> > 
> >> >>> > 
> >> >>> > On Thursday, April 12, 2018 at 8:14:42 AM UTC-4, Christoph 
> Junghans 
> >> >>> > wrote: 
> >> >>> >> 
> >> >>> >> On Thu, Apr 12, 2018 at 3:39 AM, Alexander Alexander 
> >> >>> >> <alexand...@gmail.com> wrote: 
> >> >>> >> > 
> >> >>> >> > Hi, 
> >> >>> >> > 
> >> >>> >> > I was wondering if it is normal to have table_b1,2,3,4.xvg 
> like 
> >> >>> >> > the 
> >> >>> >> > attached 
> >> >>> >> > figures? They are the result if BI (similar script as hexane 
> >> >>> >> > example) 
> >> >>> >> > over a 
> >> >>> >> > 500 ns nvt simulation of a single molecule. What could be the 
> >> >>> >> > meaning of 
> >> >>> >> > the 
> >> >>> >> > straight line passing from point (0,0) in table_b1.xvg for 
> >> >>> >> > example? 
> >> >>> >> No they don't look normal, bonded interaction should always look 
> >> >>> >> like 
> >> >>> >> an modified U with both sides, left and right, going to 
> infinity. 
> >> >>> > 
> >> >>> > 
> >> >>> > I do not know what exactly I am doing wrong; I guess the 500 ns 
> NVT 
> >> >>> > simulation is fine to get statistic for a single molecule, and 
> then 
> >> >>> > I 
> >> >>> > am 
> >> >>> > following these command in the hexane example for to obtain 
> >> >>> > bonded.xvg 
> >> >>> > potential using BI: 
> >> >>> > 
> >> >>> > #!/bin/bash -e 
> >> >>> > 
> >> >>> > #calculate bonded potentials with csg_boltzmann 
> >> >>> > 
> >> >>> > csg_boltzmann --top prdnvt.tpr --trj prdnvt.trr --cg mapp.xml 
> >> >>> > --begin 
> >> >>> > 2000 < 
> >> >>> > boltzmann_cmds 
> >> >>> > 
> >> >>> > #smooth bonded potentials 
> >> >>> > csg_call --sloppy-tables table smooth bond-LG-H1.pot.ib 
> >> >>> > input_bond-LG-H1.pot 
> >> >>> > csg_call --sloppy-tables table smooth bond-H1-H2.pot.ib 
> >> >>> > input_bond-H1-H2.pot 
> >> >>> > csg_call --sloppy-tables table smooth bond-H2-L.pot.ib 
> >> >>> > input_bond-H2-L.pot 
> >> >>> > csg_call --sloppy-tables table smooth bond-L-RG.pot.ib 
> >> >>> > input_bond-L-RG.pot 
> >> >>> > csg_call --sloppy-tables table smooth angle-LG-H1-H2.pot.ib 
> >> >>> > input_angle-LG-H1-H2.pot 
> >> >>> > csg_call --sloppy-tables table smooth angle-H1-H2-L.pot.ib 
> >> >>> > input_angle-H1-H2-L.pot 
> >> >>> > csg_call --sloppy-tables table smooth angle-H2-L-RG.pot.ib 
> >> >>> > input_angle-H2-L-RG.pot 
> >> >>> > csg_call --sloppy-tables table smooth dihedral-LG-H1-H2-L.pot.ib 
> >> >>> > input_dihedral-LG-H1-H2-L.pot 
> >> >>> > csg_call --sloppy-tables table smooth dihedral-H1-H2-L-RG.pot.ib 
> >> >>> > input_dihedral-H1-H2-L-RG.pot 
> >> >>> > 
> >> >>> > #convert bonded potentials to GROMACS tables 
> >> >>> > if [ -d table ]; then 
> >> >>> >   rm -r table 
> >> >>> > fi 
> >> >>> > mkdir table 
> >> >>> > 
> >> >>> > csg_call --ia-type bond --ia-name bond-LG-H1 --options 
> >> >>> > bond-LG-H1.xml 
> >> >>> > convert_potential gromacs --clean input_bond-LG-H1.pot 
> >> >>> > table/table_b1.xvg 
> >> >>> > csg_call --ia-type bond --ia-name bond-H1-H2 --options 
> >> >>> > bond-H1-H2.xml 
> >> >>> > convert_potential gromacs --clean input_bond-H1-H2.pot 
> >> >>> > table/table_b2.xvg 
> >> >>> > csg_call --ia-type bond --ia-name bond-H2-L --options 
> bond-H2-L.xml 
> >> >>> > convert_potential gromacs --clean input_bond-H2-L.pot 
> >> >>> > table/table_b3.xvg 
> >> >>> > csg_call --ia-type bond --ia-name bond-L-RG --options 
> bond-L-RG.xml 
> >> >>> > convert_potential gromacs --clean input_bond-L-RG.pot 
> >> >>> > table/table_b4.xvg 
> >> >>> > csg_call --ia-type angle --ia-name angle-LG-H1-H2 --options 
> >> >>> > angle-LG-H1-H2.xml convert_potential gromacs --clean 
> >> >>> > input_angle-LG-H1-H2.pot table/table_a1.xvg 
> >> >>> > csg_call --ia-type angle --ia-name angle-H1-H2-L --options 
> >> >>> > angle-H1-H2-L.xml 
> >> >>> > convert_potential gromacs --clean input_angle-H1-H2-L.pot 
> >> >>> > table/table_a2.xvg 
> >> >>> > csg_call --ia-type angle --ia-name angle-H2-L-RG --options 
> >> >>> > angle-H2-L-RG.xml 
> >> >>> > convert_potential gromacs --clean input_angle-H2-L-RG.pot 
> >> >>> > table/table_a3.xvg 
> >> >>> > csg_call --ia-type angle --ia-name dihedral-LG-H1-H2-L --options 
> >> >>> > dihedral-LG-H1-H2-L.xml convert_potential gromacs --clean 
> >> >>> > input_dihedral-LG-H1-H2-L.pot table/table_d1.xvg 
> >> >>> > csg_call --ia-type angle --ia-name dihedral-H1-H2-L-RG --options 
> >> >>> > dihedral-H1-H2-L-RG.xml convert_potential gromacs --clean 
> >> >>> > input_dihedral-H1-H2-L-RG.pot table/table_d2.xvg 
> >> >>> > 
> >> >>> > Even I have similar problem for a molecule with three beads. 
> >> >>> > Attachment is a log.txt file out of running the above script. Any 
> >> >>> > help 
> >> >>> > would 
> >> >>> > be highly appreciated. 
> >> >>> As discussed on the mailing list in great detail, the art is to 
> pick 
> >> >>> the min and max of the potentials, so that the extrapolation is 
> >> >>> useful. 
> >> >> 
> >> >> You mean I have to edit (clip) the pot.in I get from csg_boltzmann 
> (tab 
> >> >> ....) (the first command in the above script), as bond-case.pot.in, 
> >> >> right? 
> >> >>  Actually, that is the point I am getting confused. 
> >> >> There are several min and max set in input files: 
> >> >> One min and max set is in csg_boltzmann such as: 
> >> >> tab set min XXX 
> >> >> tab set max YYY 
> >> >> 
> >> >> One is in one set of min max in the <bonded> section of bond-A-B.xml 
> >> >> feed 
> >> >> to the csg_call. like: 
> >> >> <bonded> 
> >> >>      <min>xxx</min> 
> >> >>      <max>yyy</max> 
> >> >>      <step>0.001</step> 
> >> >> </bonded> 
> >> >> Again there is another set of min max in the <inverse> section of 
> the 
> >> >> same 
> >> >> file as below: 
> >> >> <inverse> 
> >> >>                 <gromacs> 
> >> >>                         <pot_max>1e8</pot_max> 
> >> >>                         <table_end>0.4</table_end> 
> >> >>                         <table_bins>0.001</table_bins> 
> >> >>                 </gromacs> 
> >> >> </inverse> 
> >> >> 
> >> >>> You can basically not expect VOTCA will get this right 
> automatically. 
> >> >>> And nothing prevents you from doing this by hand, right? You are 
> >> >>> right. 
> >> >>> And then you can provide your hand-tuned initial guess as a pot.in 
> >> >>> file 
> >> >>> to IBI. 
> >> >> 
> >> >> Probably you mean rest of BI (like csg_call and converting to 
> >> >> table_*.xvg 
> >> >> format), because I still getting the bonded potentials using BI. And 
> >> >> the 
> >> >> final table_*.xvg are supposed be used as input for IBI. 
> >> >> 
> >> >> Best regards, 
> >> >> Alex 
> >> >>> 
> >> >>> 
> >> >>> Christoph 
> >> >>> 
> >> >>> > 
> >> >>> > BTW, how the form of the angle-bonded potential should look like? 
> >> >>> > The 
> >> >>> > table_a1.xvg for hexane does not go to +infinity from the right 
> leg. 
> >> >>> > Thank you. 
> >> >>> > Regards, 
> >> >>> > Alex 
> >> >>> > 
> >> >>> >> 
> >> >>> >> > Also, is the format of the table_bonded.xvg is "x y [error 
> bar]"? 
> >> >>> >> x,y, force - see the gromacs manual for details. 
> >> >>> >> 
> >> >>> >> Christoph 
> >> >>> >> 
> >> >>> >> > Thank you. 
> >> >>> >> > Regards, 
> >> >>> >> > Alex 
> >> >>> >> > 
> >> >>> >> > On Wednesday, April 11, 2018 at 3:44:30 PM UTC-4, Christoph 
> >> >>> >> > Junghans 
> >> >>> >> > wrote: 
> >> >>> >> >> 
> >> >>> >> >> On Wed, Apr 11, 2018 at 12:49 PM, Alexander Alexander 
> >> >>> >> >> <alexand...@gmail.com> wrote: 
> >> >>> >> >> > 
> >> >>> >> >> > Hi Christoph, 
> >> >>> >> >> > 
> >> >>> >> >> > On Wednesday, April 11, 2018 at 8:22:24 AM UTC-4, Christoph 
> >> >>> >> >> > Junghans 
> >> >>> >> >> > wrote: 
> >> >>> >> >> >> 
> >> >>> >> >> >> 
> >> >>> >> >> >> 
> >> >>> >> >> >> On Wed, Apr 11, 2018, 01:51 Alexander Alexander 
> >> >>> >> >> >> <alexand...@gmail.com> 
> >> >>> >> >> >> wrote: 
> >> >>> >> >> >>> 
> >> >>> >> >> >>> 
> >> >>> >> >> >>> Hi, 
> >> >>> >> >> >>> You mean BI over a single molecule in vacuum? 
> >> >>> >> >> >> 
> >> >>> >> >> >> 
> >> >>> >> >> >> Yes, or any potential, which has right equilibrium 
> >> >>> >> >> >> length/value. 
> >> >>> >> >> > 
> >> >>> >> >> > I decided to the BI for bonded interaction, the procedure 
> and 
> >> >>> >> >> > results 
> >> >>> >> >> > for 
> >> >>> >> >> > one of the molecule is shared in the below link, I am not 
> sure 
> >> >>> >> >> > if 
> >> >>> >> >> > everything 
> >> >>> >> >> > is fine, I would be so appreciated if you could kindly have 
> a 
> >> >>> >> >> > look 
> >> >>> >> >> > and 
> >> >>> >> >> > give 
> >> >>> >> >> > any suggestion, please. 
> >> >>> >> >> > 
> >> >>> >> >> > 
> >> >>> >> >> > 
> >> >>> >> >> > 
> https://drive.google.com/open?id=1hvIH9mk1LfYo5LOO1VjBAkBZx7L0q3P0 
> >> >>> >> >> > 
> >> >>> >> >> > Also, do the settings used in the hexane or spce water 
> example 
> >> >>> >> >> > in 
> >> >>> >> >> > the 
> >> >>> >> >> > tutorial are the real settings and parameters used in your 
> >> >>> >> >> > publication? 
> >> >>> >> >> > or 
> >> >>> >> >> > these are just examples. 
> >> >>> >> >> Most of them are, but some got adapted a bit to be more 
> >> >>> >> >> instructive 
> >> >>> >> >> as 
> >> >>> >> >> tutorials. 
> >> >>> >> >> 
> >> >>> >> >> Christoph 
> >> >>> >> >> > 
> >> >>> >> >> > Thanks. 
> >> >>> >> >> > Regards, 
> >> >>> >> >> > Alex 
> >> >>> >> >> >> 
> >> >>> >> >> >> 
> >> >>> >> >> >>> 
> >> >>> >> >> >>> Instead of sd integrater can md integrator (but still in 
> NVT 
> >> >>> >> >> >>> ensemble) 
> >> >>> >> >> >>> be 
> >> >>> >> >> >>> used in IBI ( bonded and nonbonded or either of them) and 
> >> >>> >> >> >>> still 
> >> >>> >> >> >>> have 
> >> >>> >> >> >>> good 
> >> >>> >> >> >>> results? 
> >> >>> >> >> >> 
> >> >>> >> >> >> 
> >> >>> >> >> >> Sure as long as you are still sampling NVT you can use any 
> >> >>> >> >> >> integrator. 
> >> >>> >> >> >> However, usually sd is the more stable integrator, so I 
> don't 
> >> >>> >> >> >> think 
> >> >>> >> >> >> that 
> >> >>> >> >> >> change will help with your problem. 
> >> >>> >> >> >> 
> >> >>> >> >> >> Christoph 
> >> >>> >> >> >> 
> >> >>> >> >> >>> Thanks, 
> >> >>> >> >> >>> Alex 
> >> >>> >> >> >>> 
> >> >>> >> >> >>> -- 
> >> >>> >> >> >>> 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 votca+un...@googlegroups.com. 
> >> >>> >> >> >>> To post to this group, send email to 
> vo...@googlegroups.com. 
> >> >>> >> >> >>> Visit this group at https://groups.google.com/group/votca. 
>
> >> >>> >> >> >>> For more options, visit 
> https://groups.google.com/d/optout. 
> >> >>> >> >> > 
> >> >>> >> >> > -- 
> >> >>> >> >> > 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 votca+un...@googlegroups.com. 
> >> >>> >> >> > To post to this group, send email to vo...@googlegroups.com. 
>
> >> >>> >> >> > 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 votca+un...@googlegroups.com. 
> >> >>> >> > To post to this group, send email to vo...@googlegroups.com. 
> >> >>> >> > 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 votca+un...@googlegroups.com. 
> >> >>> > To post to this group, send email to vo...@googlegroups.com. 
> >> >>> > 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 votca+un...@googlegroups.com. 
> >> > To post to this group, send email to vo...@googlegroups.com. 
> >> > 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 votca+un...@googlegroups.com <javascript:>. 
> > To post to this group, send email to vo...@googlegroups.com 
> <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 
>

-- 
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 votca+unsubscr...@googlegroups.com.
To post to this group, send email to votca@googlegroups.com.
Visit this group at https://groups.google.com/group/votca.
For more options, visit https://groups.google.com/d/optout.

Reply via email to