Dear Christoph,
Thank you for your reply, I just realized that lammps could read dihedrals
in both radian and degree.
Also, I am trying to change the extrapolation type for bonded interaction.
I am not sure how to select the extrapolation type for the setting file,
and also change the avg points. Do I have to change it in
the potential_extrapolate.sh script in the shared directory? Can I instead
add the extrapolation type and number of avg points to the setting file ?
If so, can you please help here?
<!-- Dihedral Part -->
<bonded>
<!-- name of the interaction -->
<name>dihedral.1</name>
<min>-3.14159</min>
<max>3.14159</max>
<step>0.01</step>
<inverse>
<!-- target distribution -->
<target>dihedral.1.dist.tgt</target>
<lammps>
<table>table_d1.xvg</table>
<table_begin>-3.14159</table_begin>
<table_end>3.14159</table_end>
<table_left_extrapolation> exponential </table_left_extrapolation>
<table_right_extrapolation> exponential </table_right_extrapolation>
</lammps>
</inverse>
</bonded>
Best regards
Saeed
On Tue, Jan 3, 2023 at 8:16 PM Christoph Junghans <[email protected]>
wrote:
> On Tue, Jan 3, 2023 at 9:47 AM Saeed Norouzi <[email protected]> wrote:
> >
> > Dear Christoph,
> > Thank you so much for your help. I used the <table_begin> and
> <table_end> in my setting file, and now it works. Could I also do the
> extrapolation on my target distribution, so I do not have to do it for
> every iteration and remove this interaction-specific from the setting file?
> That might work, but I am not sure! The problem with poorly sampled
> regions in IBI is that they can lead to systematic errors in the
> update.
>
> > Also, How could I have other than linear extrapolation for my data?
> Yes, there should be an option,
> inverse.lammps.table_left_exprapolation for each interaction (and same
> for right), options are constant, linear, quadratic, exponential and
> sasha. See "csg_call potential extrapolate --help" and "csg_call table
> extrapolate --help" for details.
>
> > Moreover, as you can see below, I have dihedral interaction in my
> settings file and I am trying to do ibi for this part also. but the problem
> is the VOTCA gives the potential file for dihedral in radian units not
> degree. I am using lammps and I need to have the table function in degree
> units, as VOTCA does for angle potential. Can you please help me out with
> this?
>
> Dihedrals are not fully implemented yet. But I think you could set
> inverse.lammps.scale to 180/pi=57.295 for that interaction.
>
> Christoph
>
> >
> > <!-- Dihedral Part -->
> > <bonded>
> > <!-- name of the interaction -->
> > <name>dihedral.1</name>
> > <min>-3.14159</min>
> > <max>3.14159</max>
> > <step>0.01</step>
> > <inverse>
> > <!-- target distribution -->
> > <target>dihedral.1.dist.tgt</target>
> > <lammps>
> > <table>table_d1.xvg</table>
> > <table_begin>-3.14159</table_begin>
> > <table_end>3.14159</table_end>
> > </lammps>
> > </inverse>
> > </bonded>
> >
> >
> > Best regards
> > Saeed
> >
> >
> >
> >
> >
> >
> > On Mon, Jan 2, 2023 at 4:16 PM Christoph Junghans <[email protected]>
> wrote:
> >>
> >> On Mon, Jan 2, 2023 at 7:51 AM Saeed Norouzi <[email protected]>
> wrote:
> >> >
> >> > Dear VOTCA Users,
> >> >
> >> > I am trying to use ibi for bonded interaction (bond,angle, and
> dihedral). The problem is when I am using bond distribution we do not have
> data for some ranges (like for bond distribution in this tutorial), so
> during the iteration some bonds length is bigger or smaller than the table
> outer or inner cutoff and I get error in LAMMPS. does anyone has idea what
> can I do for this error? is there any option in VOTCA to replace the zeros
> in the probability for bonds with some small values so I can increase the
> table cutoff or I should do it manually?
> >> There are interaction-specific properties inverse.lamps.table_begin
> >> and inverse.lamps.table_end that you can set for each interaction that
> >> can be smaller/ larger than VOTCA's min and max (the area where IBI is
> >> performed) . VOTCA will then do an extrapolation for that extra area.
> >>
> >> Christoph
> >> >
> >> > I am using LAMMPS for my ibi and here is an error I have currently.
> >> >
> >> > Per MPI rank memory allocation (min/avg/max) = 7.672 | 7.674 | 7.676
> Mbytes
> >> > Step Time TotEng PotEng Volume Density Temp Press
> >> > 0 0 963.12455 -1360.1188 151186.66
> 1.029793 600 -1094.7381
> >> > 2000 20 928.00314 -1457.0206 151186.66
> 1.029793 615.95537 -1217.8225
> >> > 4000 40 942.24742 -1472.8241 151186.66
> 1.029793 623.71551 917.70274
> >> > 6000 60 925.95597 -1483.2126 151186.66
> 1.029793 622.19103 3122.7127
> >> > 8000 80 921.17567 -1446.9757 151186.66
> 1.029793 611.59792 1398.679
> >> > 10000 100 972.68412 -1498.2288 151186.66
> 1.029793 638.13709 3228.6631
> >> > 12000 120 968.92421 -1504.366 151186.66
> 1.029793 638.75105 2570.6902
> >> > 14000 140 973.39445 -1546.9816 151186.66
> 1.029793 650.91141 -2645.2069
> >> > 16000 160 826.48486 -1573.7195 151186.66
> 1.029793 619.87591 164.50872
> >> > ERROR on proc 20: Bond length > table outer cutoff: type 3 length
> 4.4888905 (src/MOLECULE/bond_table.cpp:605)
> >> > Last command: run 50000
> >> >
> >> >
> >> > Best regards
> >> > Saeed
> >> >
> >> > --
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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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