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? Also, How could I
have other than linear extrapolation for my data?
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?
<!-- 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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