convert csg potential to tab

[郭志成]

Hi:

I convert the csg potential files to the tab format (as read by espresso) using table_to_tab.pl (csg_call convert_potential tab). 

However, it needed three parameters (table_to_tab.sh in_pot in_deriv_pot outfile). 

The problem is that I can not understand the meaning of in_deriv_pot. How can I obtain the in_deriv_pot? 

I will be very appreciable for any suggestion. 

[Christoph Junghans]

2013/11/5 郭志成 <zcgu...@gmail.com>:

> Hi:
>
> I convert the csg potential files to the tab format (as read by espresso)
> using table_to_tab.pl (csg_call convert_potential tab).
>
> However, it needed three parameters (table_to_tab.sh in_pot in_deriv_pot
> outfile).
>
> The problem is that I can not understand the meaning of in_deriv_pot. How
> can I obtain the in_deriv_pot?

csg_call convert_potential tab is just the low level script, which
need an extra file with the derivatives in it.

csg_call convert_potential espresso
should do what you want to do.

>
> I will be very appreciable for any suggestion.
>

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

[Zhicheng]

Hi Christoph:

 

Thanks for your reply. I use the 'csg_call --options table.xml --ia-type non-bonded --ia-name CG-CG convert_potential espresso CG-CG.pot tab' to convert the coarse-grained potential(CG-CG.pot) calculated by gromacs ibi procedure to espresso format(tab). However, I get the following error message:

csg_get_interaction_property: Could not get 'max' for interaction with name 'CG-CG'  from table.xml and no default was found in

/home/adminuser/votca_ctp/share/votca/xml/csg_defaults.xml Details can be found above .

 

在 2013年11月6日星期三UTC+8上午12时47分44秒，Christoph Junghans写道：

[Sikandar Mashayak]

Hi

I am trying to reproduce the error, but when I run the same command 'csg_call --options table.xml --ia-type non-bonded --ia-name CG-CG convert_potential espresso CG-CG.pot tab', the command just get stuck and I am not getting any error or any kind of output.

I am not sure why is csg_call getting stuck.

Anyway, I guess, issue of property 'max' not found is due to incomplete information in table.xml. Try using the settings.xml given in ibi_esspresso tutorial instead of your table.xml. I hope that should work well.

--

Sikandar

[Chandan Choudhury]

On Wed, Nov 6, 2013 at 9:32 PM, Sikandar Mashayak <symas...@gmail.com> wrote:

Hi

I am trying to reproduce the error, but when I run the same command 'csg_call --options table.xml --ia-type non-bonded --ia-name CG-CG convert_potential espresso CG-CG.pot tab', the command just get stuck and I am not getting any error or any kind of output.

I am not sure why is csg_call getting stuck.

Hi Sikandar,

I second your observation.

This behavior is true for the 1.3-dev version. But if I try it on 1.2.3 it executes. As I need to toggle between the two versions, this was never a problem for for me.

Chandan

[郭志成]

Hi

 

Thanks for your suggestion. For your comment, however, it is the method of calculating the coarse-grained potential using ibi procedure by espresso soft. I have obtained the coarse-grained potential (CG-CG.pot) calculated by gromacs with ibi procedure. I want to convert this potential to espresso format using csg_call convert_potential espresso. Anyway, thanks again for your reply.

2013/11/7 Chandan Choudhury <iit...@gmail.com>

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[Sikandar Mashayak]

Hi

I am sorry I was not clear in my response.

The reason for the errors was that the table.xml file provided by you did not contain all the required parameters for potential conversions to espresso potential tables. Also, the sequence of parameters inside the table.xml file was not right.

I have corrected the table.xml file, which is attached below.  May be you can compare it with earlier settings to understand what was going wrong.

I hope this helps.

Cheers
Sikandar

[郭志成]

Hi  Sikandar:

You are right. I made some mistakes about the parameters for potential conversion to espresso potential tables.

 It is working now based on youre suggestion. Thank you very much!

Best Wishes!

Zhicheng 

2013/11/13 Sikandar Mashayak <symas...@gmail.com>

[Sikandar Mashayak]

You are welcome Zhicheng.

Chandan, please pull the latest changes in votca.csg, Christoph has corrected the issue in csg_call.

---

Sikandar