About table_extrapoltaion.pl scripts

[롤롱이]

Hi, I'm using VOTCA 1.4.1 to develop polymer chain potential in water

After develop bonded & non bonded potential through IBI, I tested long simulation with developed potential and the system was exploded after 100ns

(during IBI, I tested only for 10ns, and the explosion occur at various simulation time other than 100ns)

The reason, I guess, is the dihedral potential since it has fluctuation in pot file

To solve the problem by removing fluctuation, I marked 'o' to the fluctuation value for purpose of extrapolation.

and then, I typed the command 

csg_call table  extrapolate --avgpoints 5 ABAB-dihedral.dist.tgt ABAB.dist.new

But, the input file (ABAB-dihedral.dist.tgt) is exactly same as output file(ABAB.dist.new).

when I used various options --function exponential , --avgpoints with different value, the result was same

and also I tested table extrapolate with pot file,  ABAB-dihedral.pot.raw. ,but also it gave me the same result as former.

It's weird that nothing change

The manual said,  

[4.2.3] Extrapolation

csg_call table extrapolate [options] table_resample.pot \

table_extrapolate.pot

"all values in the potential file that should be used as a basis for extrapolation

are marked with an i, while all values that need extrapolation are marked by o. The command

above now extrapolates all o values from the i values in the file."

What should I do to remove fluctuation from the dist or pot file?

The fluctuation in potential file could cause the system to be exploded?

I attached the ABAB-dihedral.dist.tgt, ABAB-dihedral.dist.extrapolate, ABAB-dihedral.pot.raw, ABAB-dihedral.pot.extrapolate 

[Christoph Junghans]

On Sun, Jun 23, 2019 at 10:35 PM 롤롱이 <parkch...@gmail.com> wrote:
>
> Hi, I'm using VOTCA 1.4.1 to develop polymer chain potential in water
>
> After develop bonded & non bonded potential through IBI, I tested long simulation with developed potential and the system was exploded after 100ns
> (during IBI, I tested only for 10ns, and the explosion occur at various simulation time other than 100ns)
>
> The reason, I guess, is the dihedral potential since it has fluctuation in pot file
>
> To solve the problem by removing fluctuation, I marked 'o' to the fluctuation value for purpose of extrapolation.
>
> and then, I typed the command
> csg_call table extrapolate --avgpoints 5 ABAB-dihedral.dist.tgt ABAB.dist.new
>
> But, the input file (ABAB-dihedral.dist.tgt) is exactly same as output file(ABAB.dist.new).
>
> when I used various options --function exponential , --avgpoints with different value, the result was same
>
> and also I tested table extrapolate with pot file, ABAB-dihedral.pot.raw. ,but also it gave me the same result as former.
>
> It's weird that nothing change
>
> The manual said,
>
> [4.2.3] Extrapolation
> csg_call table extrapolate [options] table_resample.pot \
> table_extrapolate.pot
>
> "all values in the potential file that should be used as a basis for extrapolation
> are marked with an i, while all values that need extrapolation are marked by o. The command
> above now extrapolates all o values from the i values in the file."

Only the first interval of "i" values get picked up, so you cannot put
"o" in the middle of the file.

>
>
> What should I do to remove fluctuation from the dist or pot file?

There is also a smoothing update you could try.

>
> The fluctuation in potential file could cause the system to be exploded?

Maybe, that depends on your system.

Christoph

>
> I attached the ABAB-dihedral.dist.tgt, ABAB-dihedral.dist.extrapolate, ABAB-dihedral.pot.raw, ABAB-dihedral.pot.extrapolate
>

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--
Christoph Junghans
Web: http://www.compphys.de

[롤롱이]

Thanks for reply!

2019년 6월 26일 수요일 오전 12시 9분 10초 UTC+9, Christoph Junghans 님의 말:

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