On Thu, Apr 12, 2018 at 9:57 AM, Alexander Alexander
<alexanderwie...@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 can basically not expect VOTCA will get this right automatically.
And nothing prevents you from doing this by hand, right?
And then you can provide your hand-tuned initial guess as a pot.in file to IBI.

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+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.



-- 
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