Mapping Block-copolymer

[Pratyasha Bhardwaj]

Dear Users,

How do I map a block copolymer in votca? My all-atom system has PE- PEG copolymer chains and water. Since PE and PEG are bonded to each other , how do I define the mapping file? What do I put in the 'ident' tag in the xml file.

Could you please help me out?

Thank You

Pratyasha

[Christoph Junghans]

On Sun, Feb 4, 2024 at 8:16 AM Pratyasha Bhardwaj
<pratya...@gmail.com> wrote:
>
> Dear Users,
>
> How do I map a block copolymer in votca? My all-atom system has PE- PEG copolymer chains and water. Since PE and PEG are bonded to each other , how do I define the mapping file?

See here: https://www.votca.org/csg/input_files.html#mapping-files

> What do I put in the 'ident' tag in the xml file.

It is the name of the molecule from the topology file.

> Could you please help me out?

You could try to use Stock as well: http://stock.cmm.ki.si/smt/

Christoph
>
> Thank You
> Pratyasha
>
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--
Christoph Junghans
Web: http://www.compphys.de

[Pratyasha Bhardwaj]

Dear Christoph,

Thank you for the quick reply. What I meant is I have a gro file where the PE molecules are named as PEX , PEY and so on, each having different length and then I have PEG molecule. I have bonds between the different PE and PEG chains forming a large copolymer chain. If I define one mapping file per molecule, how will I account for the bonds between these different molecules.

Thank you

Pratyasha

[Christoph Junghans]

On Sun, Feb 4, 2024 at 9:47 AM Pratyasha Bhardwaj
<pratya...@gmail.com> wrote:
>
> Dear Christoph,
>
> Thank you for the quick reply. What I meant is I have a gro file where the PE molecules are named as PEX , PEY and so on, each having different length and then I have PEG molecule. I have bonds between the different PE and PEG chains forming a large copolymer chain. If I define one mapping file per molecule, how will I account for the bonds between these different molecules.

Votca doesn't support bonds between different molecules, but you can
also map the PE* parts separately and then reintroduce the bonds in
the coarse-grained topology by hand.

Christoph

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/602715f2-74b7-4f87-8a83-58111d8a5b91n%40googlegroups.com.

[Pratyasha Bhardwaj]

Dear Christopher,

I have made all the mapping files. I have a total of 5 different molecules, namely: PEW,PEX,PEY,PEZ(all polyethylene molecules) and PEG. I haven't defined the bonds in coarse-grained topology yet as you mentioned above. 

However, when I try to use the csg_map function -> csg_map --top new.tpr --trj changedALL.gro --cg "PEG.xml;PEX.xml;PEY.xml;PEZ.xml;PEW.xml" --out conf_cg.gro, I get this error: WARNING: unknown molecule "Other_chain_A" with id 2817 in topology
molecule will not be mapped to CG representation
Check weather a mapping file for all molecule exists, was specified in --cg separated by ; and the ident tag in xml-file matches the molecule name

During creation of topology, I had created 2 itp files that contains the topology information. I am attaching those itp files as well as all other files used in the command. Can you point out where I might be making a mistake as I have defined all the molecules.
Since the gro file is exceeding the upload limit. I am attaching a link for the gro file and tpr file :https://drive.google.com/drive/u/0/folders/10MOUsNZqZctHYm8ithO7wndp1rzaQiAe

Sincerely,
Pratyasha

[Christoph Junghans]

On Tue, Mar 12, 2024 at 12:03 AM Pratyasha Bhardwaj
<pratya...@gmail.com> wrote:
>
> Dear Christopher,
>
> I have made all the mapping files. I have a total of 5 different molecules, namely: PEW,PEX,PEY,PEZ(all polyethylene molecules) and PEG. I haven't defined the bonds in coarse-grained topology yet as you mentioned above.
> However, when I try to use the csg_map function -> csg_map --top new.tpr --trj changedALL.gro --cg "PEG.xml;PEX.xml;PEY.xml;PEZ.xml;PEW.xml" --out conf_cg.gro, I get this error: WARNING: unknown molecule "Other_chain_A" with id 2817 in topology
> molecule will not be mapped to CG representation
> Check weather a mapping file for all molecule exists, was specified in --cg separated by ; and the ident tag in xml-file matches the molecule name

It is a warning about an unmapped molecule just ignore it, if you
don't want "Other_chain_A" be mapped otherwise you will have to create
one more xml file.

Chirstoph

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/3afac3ac-678a-42ff-818c-9d25b693643an%40googlegroups.com.

[Pratyasha Bhardwaj]

Dear Christopher,

Other_chain_A is actually the name of the all-atom topology file(It has the .itp extension). It is not a molecule, it is the name of the file that contains all information regarding the PEX,PEY,PEZ,PEW and PEG molecules. 
When I do csg_dump --top new.tpr, I have the following output(a portion of that):
molecule: 255 Other_chain_B beads: 123
31242 Name 1:PEX:CA Type CT3 Mass 12.011 Resnr 0 Resname PEX Charge -0.27
31243 Name 1:PEX:HA1 Type HA3 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
31244 Name 1:PEX:HA2 Type HA3 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
31245 Name 1:PEX:HA3 Type HA3 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
31246 Name 1:PEX:CB Type CT2 Mass 12.011 Resnr 0 Resname PEX Charge -0.18
31247 Name 1:PEX:HB1 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
31248 Name 1:PEX:HB2 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
31249 Name 1:PEX:CC Type CT2 Mass 12.011 Resnr 0 Resname PEX Charge -0.18
31250 Name 1:PEX:HC1 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
31251 Name 1:PEX:HC2 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
31252 Name 1:PEX:CD Type CT2 Mass 12.011 Resnr 0 Resname PEX Charge -0.18
31253 Name 1:PEX:HD1 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
31254 Name 1:PEX:HD2 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
31255 Name 1:PEX:CE Type CT2 Mass 12.011 Resnr 0 Resname PEX Charge -0.18
31256 Name 1:PEX:HE1 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
31257 Name 1:PEX:HE2 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
31258 Name 1:PEX:CF Type CT2 Mass 12.011 Resnr 0 Resname PEX Charge -0.18
31259 Name 1:PEX:HF1 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
31260 Name 1:PEX:HF2 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
31261 Name 1:PEX:CG Type CT2 Mass 12.011 Resnr 0 Resname PEX Charge -0.18
And hence in the end, I obtain a msg  'I have 0 beads in 0 molecules for the coarsegraining'
How do I fix this? Should I use the 2 .itp files I have in place of the .tpr file I have been using?

Thank You
Sincerely,
Pratyasha

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e67mXNkobFBazLSZD6Ht%2B4wys8%2BTvgvwBfNnLsWiTPP8Q%40mail.gmail.com.

[Christoph Junghans]

On Wed, Mar 13, 2024 at 6:17 AM Pratyasha Bhardwaj
<pratya...@gmail.com> wrote:
>
> Dear Christopher,
>

> Other_chain_A is actually the name of the all-atom topology file(It has the .itp extension). It is not a molecule, it is the name of the file that contains all information regarding the PEX,PEY,PEZ,PEW and PEG molecules.
> When I do csg_dump --top new.tpr, I have the following output(a portion of that):
> molecule: 255 Other_chain_B beads: 123

Looks like the molecule is named "Other_chain_B".

> 31242 Name 1:PEX:CA Type CT3 Mass 12.011 Resnr 0 Resname PEX Charge -0.27
> 31243 Name 1:PEX:HA1 Type HA3 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31244 Name 1:PEX:HA2 Type HA3 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31245 Name 1:PEX:HA3 Type HA3 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31246 Name 1:PEX:CB Type CT2 Mass 12.011 Resnr 0 Resname PEX Charge -0.18
> 31247 Name 1:PEX:HB1 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31248 Name 1:PEX:HB2 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31249 Name 1:PEX:CC Type CT2 Mass 12.011 Resnr 0 Resname PEX Charge -0.18
> 31250 Name 1:PEX:HC1 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31251 Name 1:PEX:HC2 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31252 Name 1:PEX:CD Type CT2 Mass 12.011 Resnr 0 Resname PEX Charge -0.18
> 31253 Name 1:PEX:HD1 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31254 Name 1:PEX:HD2 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31255 Name 1:PEX:CE Type CT2 Mass 12.011 Resnr 0 Resname PEX Charge -0.18
> 31256 Name 1:PEX:HE1 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31257 Name 1:PEX:HE2 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31258 Name 1:PEX:CF Type CT2 Mass 12.011 Resnr 0 Resname PEX Charge -0.18
> 31259 Name 1:PEX:HF1 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31260 Name 1:PEX:HF2 Type HA2 Mass 1.008 Resnr 0 Resname PEX Charge 0.09
> 31261 Name 1:PEX:CG Type CT2 Mass 12.011 Resnr 0 Resname PEX Charge -0.18
> And hence in the end, I obtain a msg 'I have 0 beads in 0 molecules for the coarsegraining'
> How do I fix this? Should I use the 2 .itp files I have in place of the .tpr file I have been using?

VOTCA can only read tpr files, another option is to write your own
topology.xml file.

Christoph

> To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAOq_SnXEsqVXceQ9LGyLKELW4eGmP8-D6YUvTVrFddwBNobFDA%40mail.gmail.com.

[Pratyasha Bhardwaj]

Dear Christoph,

Thank you for pointing it out. I have for now modified my molecule names as Other_chain_A/B and got my first cg structure. I will try making my own topology.xml too. 

Sincerely,

Pratyasha

To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e46m-XqR2GdZ%2BPxq%3DWAimQrXrskuouhSoWp%3Di%2B6Wsw5mg%40mail.gmail.com.