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
> <[email protected] <javascript:>> 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
> >> <[email protected]> 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
> >> >> <[email protected]> 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
> >> >> >> <[email protected]>
> >> >> >> 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
> >> >> >>>
> >> >> >>> --
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> >> >>
> >> >>
> >> >> --
> >> >> Christoph Junghans
> >> >> Web: http://www.compphys.de
> >> >
> >> > --
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> >>
> >>
> >>
> >> --
> >> Christoph Junghans
> >> Web: http://www.compphys.de
> >
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>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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